Name |
Category |
Organism |
Program, Pipeline Name or Method Name |
Source Name |
Download link |
|
RepeatModeler Repeats |
Genome structure |
Soybean Cyst Nematode (v2) |
Standard repeatmodeler and repeatmasker pipeline |
H. glycines Genome Repeatmodeler Repeats |
genome738sl.polished.mitofixed.fa_.out_sorted.gff_.gz |
View on JBrowse |
PA3 Transcriptome on susceptible and resistant soybean |
Transcripts |
Soybean Cyst Nematode (v2) |
Trinity transcriptome with Gmap alignment |
PA3 H. glycines transcriptome. Grown on susceptible and resistant soybean cultivars |
nematode_transcripts_trinity.fasta_sorted_sorted.gff_.gz |
View on JBrowse |
Consensus Isoseq Transcriptome from PA3 and TN19 |
Transcripts |
Soybean Cyst Nematode (v2) |
SmartPortal, Gmap |
H.glycines Isoseq Consensus isoforms |
genome738sl.polished.consensus_isoforms_sorted.gff_.gz |
View on JBrowse |
NCBI Nucleotide Database Entries |
Genes |
Soybean Cyst Nematode (v2) |
Gmap |
NCBI Nucleotide entries for H. glycines |
nucleotide_mapped_sorted_sorted.gff_.gz |
View on JBrowse |
NCBI EST Database Entries |
Transcripts |
Soybean Cyst Nematode (v2) |
Gmap |
NCBI EST entries for H. glycines |
ests_mapped_sorted_gff_sorted_sorted.gff_.gz |
View on JBrowse |
Globodera rostochiensis Synteny with H.glycines |
Genome structure |
Soybean Cyst Nematode (v2) |
Opscan ortholog calling, iadhore syntenic fragment |
H. glycines synteny with G. rostochiensis genome (2016) |
rostochiensis_syntenic_ribbons_txt_gfffixed_sorted.gff_.gz |
View on JBrowse |
Tandem Duplications |
Genome structure |
Soybean Cyst Nematode (v2) |
Red Tandem used one scaffold at a time |
H. glycines genomic tandem duplications |
redtandemalljbrowsesort.bed.gz |
View on JBrowse |
High Confidence Horizontal Gene Transfers |
Genes |
Soybean Cyst Nematode (v2) |
H. glycines high confidence HGT |
H. glycines high confidence HGT |
highconfhgtsorted.bed.gz |
View on JBrowse |
Meloidogyne Incognita Syntenic Regions |
Genome structure |
Soybean Cyst Nematode (v2) |
Opscan ortholog calling, iadhore syntenic fragment |
H. glycines synteny with M. incognita genome (2016) |
incognita_syntenic_ribbons_txt_gff_sorted.gff_.gz |
View on JBrowse |
80 Effector MEME->FIMO motifs |
Genes |
Soybean Cyst Nematode (v2) |
MEME of 80 effector proteins, Genes with protein motifs found with FIMO |
Effector Motifs from the 80 known motifs |
fimogenessorted.bed.gz |
View on JBrowse |
80 Published Effectors Nucleotide Alignment (GMAP) |
Genes |
Soybean Cyst Nematode (tn10) |
Gmap Alignment of 80 Published Effectors |
Nucleotide alignment with Gmap, default parameters |
gmapeffectors.gff_.gz |
View on JBrowse |
Globodera ellingtonae Synteny with H.glycines |
Genome structure |
Soybean Cyst Nematode (v2) |
Braker,Opscan ortholog calling, iadhore syntenic fragment |
H. glycines synteny with G. ellingtonae genome (2017) |
ellingtonae_syntenic_ribbons_txt_gff_sorted.gff_.gz |
View on JBrowse |
Meloidogyne hapla Synteny with H.glycines |
Genome structure |
Soybean Cyst Nematode (v2) |
Opscan ortholog calling, iadhore syntenic fragment |
H. glycines synteny with M. hapla genome (2008) |
hapla_syntenic_ribbons_txt_gff_sorted.gff_.gz |
View on JBrowse |
Globodera pallida Synteny with H.glycines |
Genome structure |
Soybean Cyst Nematode (v2) |
Opscan ortholog calling, iadhore syntenic fragment |
H. glycines synteny with G. pallida genome (2017) |
pallida_syntenic_ribbons_sorted_txt_gff_sorted.gff_.gz |
View on JBrowse |
Meloidogyne and Globodera Synteny with H.glycines |
Genome structure |
Soybean Cyst Nematode (v2) |
Opscan ortholog calling, iadhore syntenic fragment from multiple species merged with bedtools |
H. glycines synteny with 3 Globodera and 2 Meloidogyne species |
all.synteny_sorted.gff_.gz |
View on JBrowse |
LTR Retroelements |
Genome structure |
Soybean Cyst Nematode (v2) |
LTRFinder, RepeatModeler, RepeatMasker, Bedtools Intersect |
Full length LTR models merged with bedtools. Only those that overlap with repeatmodeler repeats, merged with bed |
ltrretroelementsclassifiedcut_sorted.gff_.gz |
View on JBrowse |
DNA Transposons |
Genome structure |
Soybean Cyst Nematode (v2) |
Inverted Repeat Finder,Repeatmodeler, RepeatMasker, Bedtools |
Full length TIR pairs models merged with bedtools. Only those that overlap with repeatmodeler repeats, merged with bed |
supportedirfmergeclassifiedscnbasesorted.bed.gz |
View on JBrowse |
Pre-parasitic J2 (PA3) Biorep 1 |
Gene expression |
Soybean Cyst Nematode (v2) |
hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig |
Pre-parasitic J2 (PA3) Biorep 1 |
sortedppj2_pa3_tagctt.bam.bw |
View on JBrowse |
Helitrons |
Genome structure |
Soybean Cyst Nematode (v2) |
Helitron Scanner |
HelitronScanner default on H. glycines genome |
helitronnamedsorted.bed.gz |
View on JBrowse |
Genes with promoters containing DOG-box motifs |
Genes |
Soybean Cyst Nematode (v2) |
MEME to find Dog Box, BLAST to align GS-like effectors |
H.glycines Dog-box genes |
dorsal-likegenessorted.bed.gz |
View on JBrowse |
SNPs across 15 populations of H.glycines |
Molecular markers (QTL) |
Soybean Cyst Nematode (v2) |
GATK Best Practices: BWA-mem, Picard, GATK |
SNPs called from 15 populations of H. glycines |
sortedrenamed.combined_variants.vcf.gz |
View on JBrowse |
Alignment of 80 published known effector genes (gff3) |
Genes |
Soybean Cyst Nematode (v2) |
Gmap alignment with default parameters |
80 Known effectors Thomas Baum Lab |
test2.gz |
View on JBrowse |
Falcon Assembled Pacbio RS II subreads (pReads) |
Genome structure |
Soybean Cyst Nematode (v2) |
Blasr mapping of Pacbio preads to H.glycines genome |
Pacbio pread mapping to genome |
preads2genomegff.gz |
View on JBrowse |
Circular Consensus Pacbio RS II subreads (CCS Reads) |
Genome structure |
Soybean Cyst Nematode (v2) |
Blasr mapping of CCS Pacbio reads |
circular consensus reads assembled with smrtanalysis_2.3.0.140936. |
ccs2genome.gff_.gz |
View on JBrowse |
Camtech Raw Pacbio RS II subreads |
Genome structure |
Soybean Cyst Nematode (v2) |
Blasr mapping of raw Pacbio subreads |
Raw Pacbio subreads (TN10) |
subreads2genome.gff_.gz |
View on JBrowse |
W82_PA3_Eggs Isoseq reads |
Gene expression |
Soybean Cyst Nematode (v2) |
SmartPortal, Gmap |
IDX1 Isoseq Baum/Severin |
sortedidx1_isoforms_present.bed.gz |
View on JBrowse |
W82_PA3_J2/J3 Isoseq reads |
Gene expression |
Soybean Cyst Nematode (v2) |
SmartPortal, Gmap |
IDX2 Isoseq Baum/Severin |
sortedidx2_isoforms_present.bed.gz |
View on JBrowse |
W82_PA3_J4/Adult Isoseq reads |
Gene expression |
Soybean Cyst Nematode (v2) |
SmartPortal, Gmap |
IDX3 Isoseq Baum/Severin |
sortedidx3_isoforms_present.bed.gz |
View on JBrowse |
W82_TN19_Eggs Isoseq reads |
Gene expression |
Soybean Cyst Nematode (v2) |
SmartPortal, Gmap |
IDX4 Isoseq Baum/Severin |
sortedidx4_isoforms_present.bed.gz |
View on JBrowse |
W82_TN19_J4/Adult Isoseq reads |
Gene expression |
Soybean Cyst Nematode (v2) |
SmartPortal, Gmap |
IDX5 Isoseq Baum/Severin |
sortedidx5_isoforms_present.bed.gz |
View on JBrowse |
W82_TN19_J2/J3 |
Gene expression |
Soybean Cyst Nematode (v2) |
SmartPortal, Gmap |
IDX6 Isoseq Baum/Severin |
sortedidx6_isoforms_present.bed.gz |
View on JBrowse |
Mitochondrial Genes |
Genes |
Soybean Cyst Nematode (v2) |
mitos webserver alternative flatworm |
From genome assembly |
mitochondria.gff3.gz |
View on JBrowse |
Parasitic J2 (PA3) Forrest (Resistant Soybean) Biorep 2 |
Gene expression |
Soybean Cyst Nematode (v2) |
hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig |
parasitic J2 (PA3) Race 3 Forrest (Resistant soybean cultivar) Biorep 2 |
sortedpj2_race_3.bw |
View on JBrowse |
parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 |
Gene expression |
Soybean Cyst Nematode (v2) |
hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig |
parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 |
sortedpj2_s63_tgacca.bam.bw |
View on JBrowse |
Parasitic J2 (PA3) Forrest (Resistant Soybean) Biorep 1 |
Gene expression |
Soybean Cyst Nematode (v2) |
hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig |
parasitic J2 (PA3) Race 3 Forrest (Resistant soybean cultivar) Biorep 1 |
sortedpj2_race3_forrest.bam.bw |
View on JBrowse |
Parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 2 |
Gene expression |
Soybean Cyst Nematode (v2) |
hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig |
parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 |
sortedpj2_s63_ttaggc.bam.bw |
View on JBrowse |
Pre-parasitic J2 (PA3) Biorep 2 |
Gene expression |
Soybean Cyst Nematode (v2) |
hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig |
Pre-parasitic J2 (PA3) Biorep 2 |
sortedppj2_pa3_atcacg.bam.bw |
View on JBrowse |
H.glycines genome assembly (ABLA00000000.1) synteny |
Genome structure |
Soybean Cyst Nematode (v2) |
Braker gene prediction,opscan orthologue calling, iadhore synteny |
Monsanto/JGI |
jgisynteny.bed.gz |
View on JBrowse |
CDS of V2 Gene Models |
Genes |
Soybean Cyst Nematode (v2) |
Fasta sequences of CDS V2 gene models |
From genome assembly |
gff2fasta.cds_.fasta |
|
Repeat Explorer of TN20 |
Genome structure |
Soybean Cyst Nematode (v2) |
RepeatExplorer2, GMAP |
SRR3924425 |
nononsensehashes_sorted.gff_.gz |
View on JBrowse |
Annotated Gene Models Heterodera Glycines (updated v2) |
Genes |
Soybean Cyst Nematode (v2) |
Ortholog based Manual Annotations |
Baum/Severin Labs |
reworkedfunctionalaugustus_sorted_gff0.gz |
View on JBrowse |
Predicted Proteins from V2 Gene Models |
Genes |
Soybean Cyst Nematode (v2) |
braker gene prediction, gff2fasta |
From genome assembly |
finalaugustus.pep_.fasta |
|
Annotated Braker Gene Models IPRSCAN |
Genes |
Soybean Cyst Nematode (v2) |
Interproscan, Swissprot, Uniref |
Baum/Severin Labs |
annotatedcorrectlyaugustus_sorted77.gff_.gz |
View on JBrowse |
Globodera Ellingtonae Gene Predictions |
Related species |
Soybean Cyst Nematode (v2) |
Hisat2, Braker |
Baum/Severin Labs, GCA_001723225.1, SRR3162514 |
globoderaellingtonaegenepredictions.gff_.gz |
|
24H attraction SCN exposed to roots -- SRR5447108 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447108 , Chinese Academy of Sciences |
srr5447108_1.fastq_sorted_0.bw |
View on JBrowse |
3H control SCN exposed to roots -- SRR5447119 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447119 , Chinese Academy of Sciences |
srr5447119_1.fastq_sorted_0.bw |
View on JBrowse |
3H control SCN exposed to roots -- SRR5447118 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447118 , Chinese Academy of Sciences |
srr5447118_1.fastq_sorted_1.bw |
View on JBrowse |
3H attraction SCN exposed to roots -- SRR5447117 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447117 , Chinese Academy of Sciences |
srr5447117_1.fastq_sorted_0.bw |
View on JBrowse |
24H control SCN exposed to roots -- SRR5447115 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447115 , Chinese Academy of Sciences |
srr5447115_1.fastq_sorted.bw |
View on JBrowse |
24H control SCN exposed to roots -- SRR5447114 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447114 , Chinese Academy of Sciences |
srr5447114_1.fastq_sorted_0.bw |
View on JBrowse |
SRR6230581 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230582_1_val_1.fqmRNA_sorted_4RpgMKg.bw |
View on JBrowse |
24H attraction SCN exposed to roots -- SRR5447112 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447112 , Chinese Academy of Sciences |
srr5447112_1.fastq_sorted_0.bw |
View on JBrowse |
24H attraction SCN exposed to roots -- SRR5447113 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447113 , Chinese Academy of Sciences |
srr5447113_1.fastq_sorted_0.bw |
View on JBrowse |
24H control SCN exposed to roots -- SRR5447110 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447110 , Chinese Academy of Sciences |
srr5447110_1.fastq_sorted_0.bw |
View on JBrowse |
3H control SCN exposed to roots -- SRR5447109 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447109_1 , Chinese Academy of Sciences |
srr5447109_1.fastq_sorted.bw |
View on JBrowse |
3H attraction SCN exposed to roots -- SRR5447111 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447111_1 , Chinese Academy of Sciences |
srr5447111_1.fastq_sorted.bw |
View on JBrowse |
3H attraction SCN exposed to roots -- SRR5447116 |
Gene expression |
Soybean Cyst Nematode (v2) |
Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig |
SRR5447116_1 , Chinese Academy of Sciences |
srr5447116_1.fastq_sorted_0.bw |
View on JBrowse |
Trinity Transcripts form Gardner et al 2017 |
Transcripts |
Soybean Cyst Nematode (v2) |
Gmap alignment |
NCBI Bioproject PRJNA415980 |
scngenome.gfzz01.1_sorted.gff_.gz |
View on JBrowse |
Alignments of genes producing secreted proteins |
Genes |
Soybean Cyst Nematode (v2) |
Braker genes, SignalP |
Genes with N terminal secretion signals, and lacking transmembrane domains |
reworkedfunctionalaugustussecreted_sorted.gff_.gz |
View on JBrowse |
Transcripts of genes producing secreted proteins |
Transcripts |
Soybean Cyst Nematode (v2) |
Braker genes, SignalP and Tmhmm |
Baum/Severin Labs |
secretedtranscripts.fasta |
|
Fasta sequences of the 80 published effector genes |
Transcripts |
Soybean Cyst Nematode (v2) |
Collected from literature |
Baum/Severin Labs |
effector.fasta |
|
op50 genes |
Genes |
Soybean Cyst Nematode (op50) |
Placeholder |
Rick Masonbrink |
op50_sorted.gff3.gz |
View on JBrowse |
tn7 genes |
Genes |
Soybean Cyst Nematode (tn7) |
Placeholder |
Rick Masonbrink |
tn7_sorted.gff3.gz |
View on JBrowse |
tn8canu genes |
Genes |
Soybean Cyst Nematode (tn8canu) |
Placeholder |
Rick Masonbrink |
tn8canu_sorted.gff3.gz |
View on JBrowse |
tn8 genes |
Genes |
Soybean Cyst Nematode (tn8) |
Placeholder |
Rick Masonbrink |
tn8_sorted.gff3.gz |
View on JBrowse |
tn20 genes |
Genes |
Soybean Cyst Nematode (tn20) |
Placeholder |
Rick Masonbrink |
tn20_sorted.gff3.gz |
View on JBrowse |
X12 genes |
Genes |
Soybean Cyst Nematode (X12) |
Placeholder |
Rick Masonbrink |
x12genome_sorted.gff3.gz |
View on JBrowse |
Input Transcriptome Assemblies to Final Prediction |
Genes |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
orderedmergingtestscn.gff3.resortfixed.gff_.gz |
View on JBrowse |
Published Effectors via protein-protein alignment |
Genes |
Soybean Cyst Nematode (tn10) |
Diamond Alignment of 80 Published Effectors |
Protein protein alignment with Diamond, default parameters |
diamondeffectors.gff3.gz |
View on JBrowse |
Genomethreader Alignment of X12 Annotation |
Genes |
Soybean Cyst Nematode (tn10) |
Genomethreader of Published Annotation |
Liam et al Gene Models, Masonbrink alignment |
x12genomethreader.gff_.gz |
View on JBrowse |
Repeatmasker |
Genome structure |
Soybean Cyst Nematode (tn10) |
Repeatmodeler Prediction, Repeatmasker Annotation |
Masonbrink |
repeatmasker.gff_.gz |
View on JBrowse |
NCRNAs Mikado Prediction |
Noncoding RNAs |
Soybean Cyst Nematode (tn10) |
mikado prediction of NCRNAs |
Masonbrink |
ncrnas.gff3.gz |
View on JBrowse |
EDTA Annotated Transposons |
Genome structure |
Soybean Cyst Nematode (tn10) |
EDTA Extensive Denovo Transposon Annotator |
Masonbrink |
edtatransposons1.gff3.gz |
View on JBrowse |
Ribosomal Genes |
Genome structure |
Soybean Cyst Nematode (tn10) |
BLAST of nematode ribosomal genes from NCBI |
Masonbrink |
ribocoordsfix.bed.gz |
View on JBrowse |
Tandem Repeats Finder |
Genome structure |
Soybean Cyst Nematode (tn10) |
Tandem Repeats Finder |
Masonbrink |
sortedtrf.bed.gz |
View on JBrowse |
SVIM TN10 Pacbio Structural Variants |
Genome structure |
Soybean Cyst Nematode (tn10) |
minimap2 mapping and SVIM |
Masonbrink |
svimvariants.vcf.gz |
View on JBrowse |
TN10 SNPS/INDELS |
Molecular markers (QTL) |
Soybean Cyst Nematode (tn10) |
Freebayes 1.1.0, bcftools 1.10.2 filter |
Masonbrink |
sortscngenome.tn10sm.vcf.gz |
View on JBrowse |
TN10 H.glycines Pseudomolecule Assembly Sequence |
Genome structure |
Soybean Cyst Nematode (tn10) |
Falcon, Falcon unzip, Dovetail genomics, Sspace, Juicer/3D-DNA, pilon |
Masonbrink |
scngenome.fasta |
|
TN10 H.glycines Pseudomolecule Gene Annotation |
Genes |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
orderedscngenepredictions.gff3.gz |
View on JBrowse |
TN10 H.glycines Pseudomolecule Functional Gene Annotation |
Transcripts |
Soybean Cyst Nematode (tn10) |
Interpro, BLASTP NCBI NR, BLASTN NCBI nt, blastx, blastn, blastp to swissprot, Interproscan |
Masonbrink |
functionalannotations2.gff3.gz |
View on JBrowse |
TN10 H.glycines Pseudomolecule Transcript Sequences |
Transcripts |
Soybean Cyst Nematode (tn10) |
cufflinks 2.2.1 |
Masonbrink |
orderedscngenepredictions_transcripts.fasta |
|
TN10 H.glycines Pseudomolecule Protein Sequences |
Transcripts |
Soybean Cyst Nematode (tn10) |
cufflinks 2.2.1 |
Masonbrink |
orderedscngenepredictions_proteins.fasta |
|
Genes with transposon annotations |
Genes |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
orderedgeneswithtransposonannotations.gff3.gz |
View on JBrowse |
Genes with transposon annotations transcripts fasta |
Genes |
Soybean Cyst Nematode (tn10) |
cufflinks 2.2.1 |
Masonbrink |
geneswithtransposonannotations_transcript.fasta |
|
Genes with transposon annotations protein fasta |
Transcripts |
Soybean Cyst Nematode (tn10) |
cufflinks 2.2.1 |
Masonbrink |
geneswithtransposonannotations_protein.fasta |
|
Repetitive Genes that overlap repeatmasker |
Genes |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
orderedrepeatsbyoverlap.gff3.gz |
View on JBrowse |
Repetitive Genes that overlap repeatmasker transcript fasta |
Transcripts |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
repeatsbyoverlap_transcript.fasta |
|
Repetitive Genes that overlap repeatmasker protein fasta |
Transcripts |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
repeatsbyoverlap_protein.fasta |
|
Genes that lack expression |
Genes |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
orderednoexpressedmrnagene.gff3.gz |
View on JBrowse |
Genes that lack expression -- transcript fasta sequences |
Transcripts |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
noexpressedmrnagene_transcript.fasta |
|
Genes that lack expression -- protein fasta sequences |
Transcripts |
Soybean Cyst Nematode (tn10) |
masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks |
Masonbrink |
noexpressedmrnagene_protein.fasta |
|
SRR6230583 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230583_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR6230585 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230585_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR6230587 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230587_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR6230586 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230586_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR6230579 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230579_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR13711080 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
1703FL-02-04_S4_L001_R1_001_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR13711081 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
1703FL-02-03_S3_L001_R1_001_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR13711085 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
1703FL-02-01_S1_L001_R1_001.fastqMult_sorted.bw |
View on JBrowse |
SRR13711082 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
1703FL-02-02_S2_L001_R1_001_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR13711084 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
1703-TM101_S0_L003_R1_001_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR13711083 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
1703-TM102_S0_L003_R1_001_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR6230582 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230582_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR6230584 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230584_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |
SRR6230580 |
Gene expression |
Soybean Cyst Nematode (tn10) |
Hisat2 Alignment |
|
SRR6230580_1_val_1.fqmRNA_sorted.bw |
View on JBrowse |