User: lkianmehr
lkianmehr • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- France
- Last seen:
- an hour ago
- Joined:
- 7 months, 2 weeks ago
- Email:
- l********@unice.fr
Posts by lkianmehr
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... but I taught that tximport should be used just for summarizing transcript_id to gene_id ...
written 28 days ago by
lkianmehr • 30
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... Hello,
I have quantified piRNA and tRNA of RNA-seqs by Salmon on fasta file, now to do DGE analysis may I use numreads ? ...
written 29 days ago by
lkianmehr • 30
• updated
29 days ago by
WouterDeCoster ♦ 35k
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Comment:
C: repeatmask fasta file
... sorry for the delay, I checked repeat-mask index by Salmon, only there are 5 files, I think making index is not completely done, don't know why! just set k-mer 3 and receive this warning:
[jointLog] [warning] Entry with header [chr1] was long ...
written 4 weeks ago by
lkianmehr • 30
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... Excuse me, I am confused about choosing repeatmask fasta file from repbase, actually, I used Mouse.RepeatMasker.masked.fa from repbase to make an index by Salmon but output was incomplete, and Salmon is not able to make quantification on it, why? is the input file correct or I should choose another ...
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... Does anybody know what is the best and trustable way to concatenate different FASTA files for making them index together?
thanks in advance ...
written 5 weeks ago by
lkianmehr • 30
• updated
5 weeks ago by
Nicolas Rosewick ♦ 7.0k
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... Hello,
Does anyone know what should I do with the list of upregulated transcripts to find interaction and specific pathway between them? may I find a specific role of each one separately? is there any software or package to find ontology for the transcript? ...
written 5 weeks ago by
lkianmehr • 30
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Comment:
C: cause of unmapped short with STAR
... with adding these options -outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 , I got such results
Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped
M/hr number length uniq ...
written 6 weeks ago by
lkianmehr • 30
• updated
6 weeks ago by
Devon Ryan ♦ 86k
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... excuse me, minlen option is constant or may I change it? what it depends? ...
written 6 weeks ago by
lkianmehr • 30
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... Hello,
Does anyone know the reason for having such results, 47% are unmapped short?
need to mention I have cut the adaptors with cutadapt and trimmed them. the average length of reads is between 50-94.
Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped
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... thank you for comment, yes I tried to compare D ( plus D1 and D3) versus R ( plus R1 and R3). ...
written 6 weeks ago by
lkianmehr • 30
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