User: trakhtenberg

gravatar for trakhtenberg
trakhtenberg150
Reputation:
150
Status:
Trusted
Location:
United States
Last seen:
11 months, 3 weeks ago
Joined:
4 years, 7 months ago
Email:
t***********@gmail.com

Posts by trakhtenberg

<prev • 49 results • page 1 of 5 • next >
0
votes
0
answers
1.6k
views
0
answers
Upper-quartile normalization option for Cufflinks and Cuffdiff
... In the Cufflinks manual (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/#advanced-abundance-estimation-options) it says to use this command: -N/–upper-quartile-norm In the Cuffdiff manual (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#library-normalization-methods) it says to use t ...
cufflinks upper-quartile normalization cuffdiff written 2.8 years ago by trakhtenberg150
0
votes
0
answers
1.0k
views
0
answers
total-hits-norm and compatible-hits-norm default setting different in Cufflinks and Cuffdiff
... In the Cufflinks manual (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/#advanced-abundance-estimation-options) it says regarding Cufflinks options that: –compatible-hits-norm is inactive by default whereas –total-hits-norm is active by default In the Cuffdiff manual (http://cole-trapnell-l ...
cufflinks cuffdiff rna-seq written 2.8 years ago by trakhtenberg150
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Does upper-quartile normalization in Cuffdiff also normalizes by transcript leng
... Thank you for the feedback. I guess part of my confusion is the sequence of operations itself. Theoretically, the upper-quartile normalization method should be instead, not after, standard FPKM normalization. Whereas Cufflinks manual states: “FPKMs and fragment counts are scaled via the ratio of the ...
written 2.8 years ago by trakhtenberg150
1
vote
1
answer
1.1k
views
1
answer
Does upper-quartile normalization in Cuffdiff also normalizes by transcript length?
... Does upper-quartile normalization option in Cuffdiff (Cufflinks 2.2 version) also normalizes by transcript length? ...
upper-quartile normalization cuffdiff rna-seq written 2.8 years ago by trakhtenberg150 • updated 2.8 years ago by igor7.4k
1
vote
1
answer
1.2k
views
1
answer
PWF from GOseq to adjust q-value in Cuffdiff
... Hello, In accounting for gene length bias using GOseq, the PWF is used to adjust the p-value for determining the over-represented GO category. Has anyone made a script which would use this PWF for adjusting the q or p value in the Cuffdiff output files (I use cufflinks) of all DEGs? Then it would ...
gene length bias goseq rna-seq written 4.0 years ago by trakhtenberg150 • updated 4.0 years ago by Devon Ryan88k
0
votes
0
answers
2.1k
views
0
answers
GOseq and KEGG pathways analysis for mouse RNA-seq
... Hello, We did GOseq on mouse RNA-seq but are having trouble with getting the KEGG pathways analysis to work in this pipeline. It is important for us to use it in the same pipeline because GOseq accounts for the gene length bias, and it suppose to be accounted for in the KEGG pathways analysis too w ...
kegg rna-seq goseq written 4.0 years ago by trakhtenberg150 • updated 4.0 years ago by Biostar ♦♦ 20
0
votes
3
answers
1.5k
views
3
answers
Comment: C: how to export RNA-seq reads which mapped to genes?
... thank you for responding! ...
written 4.4 years ago by trakhtenberg150
0
votes
3
answers
1.5k
views
3
answers
Comment: C: how to export RNA-seq reads which mapped to genes?
... which command would you recommend for filtering the resulting SAM file? I tried converting to BAM without filtering first using this command "samtools view -bS in.sam > out.bam" but got this error: [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! I then tried "samtools vi ...
written 4.4 years ago by trakhtenberg150
0
votes
3
answers
1.5k
views
3
answers
Comment: C: how to export RNA-seq reads which mapped to genes?
... I did steps 1 and 2 but when I tried extracting the reads, I got 0.5% fewer properly paired reads than were counted by samtools flagstat in the resulting bam. Picard SamToFastq, for some reason, considered 0.5% of the reads as unpaired mates and so they had to be excluded, although they were for sur ...
written 4.4 years ago by trakhtenberg150
0
votes
3
answers
1.5k
views
3
answers
Comment: C: how to export RNA-seq reads which mapped to genes?
... samtools view -H printed this: @HD     VN:1.0  SO:queryname @SQ     SN:chr1 LN:195471971 @SQ     SN:chr10        LN:130694993 @SQ     SN:chr11        LN:122082543 @SQ     SN:chr12        LN:120129022 @SQ     SN:chr13        LN:120421639 @SQ     SN:chr14        LN:124902244 @SQ     SN:chr15        L ...
written 4.4 years ago by trakhtenberg150

Latest awards to trakhtenberg

Great Question 2.5 years ago, created a question with more than 5,000 views. For tophat output files containing the reads which mapped uniquely as a pair
Good Question 2.5 years ago, asked a question that was upvoted at least 5 times. For Extracting from tophat outputs reads pairs and splice-junctions with a single best match
Popular Question 2.5 years ago, created a question with more than 1,000 views. For GOseq and KEGG pathways analysis for mouse RNA-seq
Popular Question 2.5 years ago, created a question with more than 1,000 views. For how to export RNA-seq reads which mapped to genes?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to convert strand-specific reads to not-strand-specific format?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Identifying polyA tail sequences for predicted novel transcripts using STAR/Cufflinks
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Identifying polyA tail sequences for predicted novel transcripts using STAR/Cufflinks
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How to reduce reads in fastq, bam, bed files in a random manner?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Converting BAM to Fastq with HTSlib htscmd
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Picard error Illegal Mate State in converting BAM to Fastq
Popular Question 4.0 years ago, created a question with more than 1,000 views. For sorting merged GTFs for Tophat/Cufflinks pipeline
Supporter 4.6 years 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: 1915 users visited in the last hour