User: geo.pertea

gravatar for geo.pertea
geo.pertea60
Reputation:
60
Status:
New User
Location:
Last seen:
5 months, 3 weeks ago
Joined:
6 months, 2 weeks ago
Email:
g*********@gmail.com

Posts by geo.pertea

<prev • 4 results • page 1 of 1 • next >
0
votes
1
answer
512
views
1
answers
Answer: A: How has StringTie caculated the transcript coverage?
... Please see [this answer][1] about how coverage values are calculated by StringTie. Transcript and exon coverage values for overlapping transcripts (alternate isoforms) are calculated after distributing the read alignments according to the maximum flow algorithm -- it's not as simple as applying a fo ...
written 5 months ago by geo.pertea60
3
votes
1
answer
835
views
1
answers
Answer: A: Calculating the gene coverage in StringTie
... The coverage value shown in the output of StringTie (and in other genomics programs) is an average of all per-base coverages across the length of genomic segment (exon) or set of segments (transcript). For a gene (which is what is shown in the -A table), the union of all the exonic segments in the ...
written 5 months ago by geo.pertea60
0
votes
1
answer
1.2k
views
1
answers
Answer: A: Warning encountered while transcript abundance estimation using stringtie
... The (belated) answer to the original problem reported here can be found in this post: https://www.biostars.org/p/292650/#293209 ...
written 6 months ago by geo.pertea60
3
votes
1
answer
766
views
1
answers
Answer: A: stringtie cannot recognize Gencode GTF
... StringTie gave you an advice there, did you follow up on it? >Please make sure the -G annotation file uses the same naming convention for the genome sequences. In case you don't understand that message: it's about the chromosome names. The Gencode annotation uses chromosome names like *chr1*, * ...
written 6 months ago by geo.pertea60

Latest awards to geo.pertea

Scholar 5 months ago, created an answer that has been accepted. For A: stringtie cannot recognize Gencode GTF
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: stringtie cannot recognize Gencode GTF
Scholar 6 months ago, created an answer that has been accepted. For A: stringtie cannot recognize Gencode GTF
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: stringtie cannot recognize Gencode GTF

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 469 users visited in the last hour