User: Linda
Linda • 160
- Reputation:
- 160
- Status:
- New User
- Location:
- Last seen:
- 6 years, 10 months ago
- Joined:
- 7 years, 8 months ago
- Email:
- 1***@biostars.org
Posts by Linda
<prev
• 10 results •
page 1 of 1 •
next >
0
votes
1
answer
3.5k
views
1
answers
... Michael, thanks for taking the time to solve this. The script is from the Analysis directory in http://sourceforge.net/projects/trinityrnaseq/ Apologies for taking long to respond. ...
written 6.8 years ago by
Linda • 160
0
votes
1
answer
3.5k
views
1
answers
... I tried a putting missing NA values to 0.00 and that produced another error. Please check the edited question. Thanks for your help. ...
written 6.8 years ago by
Linda • 160
0
votes
1
answer
3.5k
views
1
answers
... I am not sure about that. I suppose the length of the transcripts comes into play since looking at the code it seems to use the Trinity.fasta file to calculate the transcript length only. ...
written 6.8 years ago by
Linda • 160
6
votes
1
answer
3.5k
views
1
answer
... I am trying to perform Differential expression using transcripts from Trinity and the edgeR package. I am essentially using the steps on http://trinityrnaseq.sourceforge.net/analysis/diff_expression_analysis.html this page. Everything goes fine until I try edgeR itself.
23:22 linda SO_564$ ~/softw ...
written 6.9 years ago by
Linda • 160
• updated
6.8 years ago by
Michael Dondrup ♦ 45k
3
votes
1
answer
1.3k
views
1
answer
... I am trying to filter the results of a paired end alignment with samtools. I would like to get all reads where both the pairs are unaligned. I tried
samtools view -f 12 R28.bam | cut -f1-9|head
HWUSI-EAS570R_0028:2:96:4625:6148#0 141 Contig18298 1907 0 100M = 1907 0
HWUSI- ...
written 7.1 years ago by
Linda • 160
• updated
7.1 years ago by
Istvan Albert ♦♦ 78k
3
votes
4
answers
69k
views
4
answers
... Yes. With some added text to identify the sequence.
...
written 7.1 years ago by
Linda • 160
3
votes
1
answer
1.5k
views
1
answer
... I have a bam file with all reads. I would like to filter out reads where both the read and its mate are unaligned. If either of them is aligned, I would like to keep both. Would
samtools view -F 12 file.bam
work?
Thanks,
...
5
votes
2
answers
3.0k
views
2
answers
... I have RNA-seq reads from a non-model organism. I used cufflinks to identify transcripts. Is there an existing pipeline to BLAST these transcripts to a model organism's proteins to identify orthologs?
...
0
votes
3
answers
10k
views
3
answers
... At this point I am looking at all the encode tfs. ...
written 7.4 years ago by
Linda • 160
12
votes
3
answers
10k
views
5 follow
3
answers
... I am interested in finding all known Transcription Factor Binding sites for a list of genes from the ENCODE dataset. How could one automate that? From the tables it appears that each TF has its own table. Thus, I could obtain promoters for my set of genes and find its intersection with the table of ...
Latest awards to Linda
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1252 users visited in the last hour