User: crimsontabaq

gravatar for crimsontabaq
crimsontabaq40
Reputation:
40
Status:
New User
Location:
Russia, Kazan Federal University
Last seen:
1 month, 2 weeks ago
Joined:
8 months, 2 weeks ago
Email:
c***********@yandex.ru

Undergrad who's trying into bioinformatic analysis of RNA-Seq data

Posts by crimsontabaq

<prev • 14 results • page 1 of 2 • next >
0
votes
3
answers
205
views
3
answers
Comment: C: 20% of unknown-source contamination RNA-Seq Illumina
... If this rate of unaligned reads is fine, am i suppose to use all reads (aligned and unaligned) in further work? ...
written 7 weeks ago by crimsontabaq40
0
votes
3
answers
205
views
3
answers
Comment: C: 20% of unknown-source contamination RNA-Seq Illumina
... I've updated the OP. How do you blast READS? There are hundreds of millions of them with the length 30-45 bp. Did you mean blasting assembled contigs? ...
written 7 weeks ago by crimsontabaq40
3
votes
3
answers
205
views
3
answers
20% of unknown-source contamination RNA-Seq Illumina
... We're working with a *de novo* transcriptome of a non-model organism. There were some genome assemblies for it, but we decided not to use it for GE analysis since they weren't annotated and also looked suspicious in some ways. Yet we've tried to map rRNA/mitRNA filtered reads on each of them and it ...
contamination rna-seq sequencing written 7 weeks ago by crimsontabaq40 • updated 7 weeks ago by Brian Bushnell13k
0
votes
1
answer
204
views
1
answers
Comment: C: EvidentialGene reduces redundancy of de novo transcriptome assembly?
... Wow, one million. Just a wild guess - have you changed min contig size in Trinity? We've adjusted this value to a minimum sized protein multiplied on 3 of relative species - mb not very right approach, but the resulting assembly is quite ok except some issues I've described earlier. ...
written 7 weeks ago by crimsontabaq40
0
votes
1
answer
204
views
1
answers
Comment: C: EvidentialGene reduces redundancy of de novo transcriptome assembly?
... Hello Pablo! We've just used one of the Evigene scripts that are supplied in the project data. We've looked through configs and didn't find anything related to our job, so we just fed the needed options to the script itself on the run. ...
written 7 weeks ago by crimsontabaq40
0
votes
1
answer
204
views
1
answers
Comment: C: EvidentialGene reduces redundancy of de novo transcriptome assembly?
... Hello and thanks for an expertized comment! I've got your points for missing prots, but could you comment on excessive annotation which we're trying to reduce? Does tr2aacds really suits for this job? We've set the configs to Evigene script according to our task, but we didn't know that it's poss ...
written 7 weeks ago by crimsontabaq40
3
votes
1
answer
204
views
5 follow
1
answer
EvidentialGene reduces redundancy of de novo transcriptome assembly?
... Hi! Since trinity output assembly ('original') has had a lot of duplicated matches with BLASTx, we decided to try reducing redundancy with tr2aacds script from [EvidentialGene][1] project. tr2aacds filters and merges contigs according to their coding potential and % of identity - sounds more legit ...
assembly transcriptome rna-seq trinity redundancy written 8 weeks ago by crimsontabaq40 • updated 7 weeks ago by gilbert.bionet60
0
votes
1
answer
184
views
1
answers
Comment: C: GSEA produces too few enriched sets
... We blastx'ed our transcripts against proteins of a relative organism, which genes are classified into KEGG pathways, so we can now group matching transcripts to these pathways. There's strong evidence for some groups to be enriched with DEGs based on previous experiments, but they ain't. ...
written 8 weeks ago by crimsontabaq40
0
votes
1
answer
184
views
1
answer
GSEA produces too few enriched sets
... Here's a transcriptome of a non-model organism. Comparing two conditions, kallisto generated ~6000 differentially expressed genes. KEGG metabolic pathways of a relative organism were used to classify DEGs and check pathways enrichment. These categories are relatively small (3-100 genes/set). Whilst ...
kallisto gsea transcriptome written 9 weeks ago by crimsontabaq40 • updated 8 weeks ago by kristoffer.vittingseerup190
1
vote
1
answer
433
views
1
answers
Comment: C: Duplicated terminal-version BLAST results
... It works! with latest blast: blastx -db BlastDB -query assembly.fa -max_target_seqs 1 -max_hsps 1 -num_threads 8 -evalue 1e-6 -outfmt 6 This job gave me little bit more results than blast-2.2.28 output sorted with 'uniq' command, yet without any double-hsps. Dziękuję! ...
written 8 months ago by crimsontabaq40

Latest awards to crimsontabaq

Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 593 users visited in the last hour