User: lkianmehr

gravatar for lkianmehr
lkianmehr30
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

<prev • 66 results • page 1 of 7 • next >
0
votes
2
answers
119
views
2
answers
Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... but I taught that tximport should be used just for summarizing transcript_id to gene_id ...
written 28 days ago by lkianmehr30
0
votes
2
answers
119
views
2
answers
May I use numreads for doing DGE after quantifying by Salmon
... Hello, I have quantified piRNA and tRNA of RNA-seqs by Salmon on fasta file, now to do DGE analysis may I use numreads ? ...
salmon dge written 29 days ago by lkianmehr30 • updated 29 days ago by WouterDeCoster35k
0
votes
0
answers
125
views
0
answers
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 lkianmehr30
0
votes
0
answers
125
views
0
answers
repeatmask fasta file
... 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 ...
teelements salmon repeatmask index written 5 weeks ago by lkianmehr30 • updated 28 days ago by Biostar ♦♦ 20
6
votes
2
answers
110
views
2
answers
How do concatenate different fasta file
... Does anybody know what is the best and trustable way to concatenate different FASTA files for making them index together? thanks in advance ...
fasta concatenate written 5 weeks ago by lkianmehr30 • updated 5 weeks ago by Nicolas Rosewick7.0k
0
votes
0
answers
89
views
0
answers
How can I find functional role and interactions between differential expressed transcripts
... 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? ...
ontology ncrna transcript rna-seq written 5 weeks ago by lkianmehr30
0
votes
2
answers
143
views
2
answers
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 lkianmehr30 • updated 6 weeks ago by Devon Ryan86k
0
votes
0
answers
255
views
0
answers
Comment: C: Problem mapping mRNA seq data using STAR.
... excuse me, minlen option is constant or may I change it? what it depends? ...
written 6 weeks ago by lkianmehr30
2
votes
2
answers
143
views
2
answers
cause of unmapped short with STAR
... 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 ...
star rna-seq written 6 weeks ago by lkianmehr30 • updated 6 weeks ago by swbarnes24.5k
0
votes
2
answers
157
views
2
answers
Comment: C: which package should be selected for differential gene expression analysis
... 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 lkianmehr30

Latest awards to lkianmehr

Supporter 5 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1745 users visited in the last hour