User: komal.rathi
komal.rathi • 3.3k
- Reputation:
- 3,340
- Status:
- Trusted
- Location:
- Children's Hospital of Philadelphia, Philadelphia, PA
- Website:
- https://github.com/kom...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 2 hours ago
- Joined:
- 5 years, 9 months ago
- Email:
- k**********@gmail.com
Posts by komal.rathi
<prev
• 410 results •
page 1 of 41 •
next >
0
votes
2
answers
1.4k
views
2
answers
... I ended up doing a chisq test using the output of ASEReadCounter. ...
written 6 days ago by
komal.rathi • 3.3k
0
votes
0
answers
738
views
0
answers
Comment:
C: RSEM output interpretation
... I am using the following parameters:
rsem-calculate-expression \
--paired-end \
--no-bam-output \
--quiet \
--no-qualities \
-p {threads} \
--forward-prob 0.5 \
--seed-length 25 \
--fragment-length-mean -1.0 \
--bam {bam} {genomedir} {prefix} ...
written 12 weeks ago by
komal.rathi • 3.3k
0
votes
1
answer
241
views
1
answers
... I don't get it. My question is what are those samples with `Molecular Data Type != RNA Seq (NGS)`? Are those also RNA-sequencing? If not, then why is the `Assay Type = RNA-Seq`? ...
written 5 months ago by
komal.rathi • 3.3k
0
votes
1
answer
241
views
1
answer
... Hi everyone,
I have dbGaP metadata for a project that has multiple datatypes (WES, WGS, RNA-seq etc) and I am trying to select only samples corresponding to RNA-seq but I am quite confused looking at a few columns in the metadata. Here are the columns:
> plyr::count(dat[,c('Assay_Type_s','a ...
written 5 months ago by
komal.rathi • 3.3k
• updated
5 months ago by
Santosh Anand ♦ 4.4k
0
votes
1
answer
585
views
1
answers
... Thank you very much for the explanation!! ...
written 16 months ago by
komal.rathi • 3.3k
0
votes
1
answer
1.1k
views
1
answers
... Yes - I am giving it a try. I thought I could just use htseq-count - but after reading up on the docs and from Simon himself - it is not possible to get exon level counts using htseq-count. ...
written 16 months ago by
komal.rathi • 3.3k
4
votes
1
answer
585
views
1
answer
... Disclaimer: Tried to post this on bioconductor support but it wont allow me. I tried adding an entire paragraph in "English language" but no - still wouldn't allow me.
Hi everyone,
I am using DEXSeq for exon quantification. I ran dexseq_prepare_annotation to convert gencode v24 GTF to GFF like thi ...
written 16 months ago by
komal.rathi • 3.3k
• updated
16 months ago by
Devon Ryan ♦ 87k
0
votes
1
answer
659
views
1
answers
... Thanks I just thought it would be simpler than this. I was hoping something like a partial match would work.. ...
written 16 months ago by
komal.rathi • 3.3k
1
vote
1
answer
659
views
1
answer
... Hi everyone,
This is a sorted bam (by coordinates):
samtools view 7316-161-T_Aligned.out.sorted.bam | grep 'FCC78FRACXX:1:1101:6639:75204'
FCC78FRACXX:1:1101:6639:75204# 163 chr2 74156623 255 23M2445N77M = 74159237 8677 CGCCTATCAATCAGATTAAACTCCTGAACAAAGAAAATAAAGTGCTTAAAGGAGGTGTTGAGGTGGGCC ...
written 16 months ago by
komal.rathi • 3.3k
0
votes
1
answer
1.1k
views
1
answers
... Oh I just realized I don't have the `exon_id` columns in the gff while I am passing `exon_id` to -i parameter in htseq-count. How do I get the exon_ids in the gff? According to [this][1] thread it is not that straightforward to get exon level counts using htseq-count.
[1]: http://seqanswers.com/ ...
written 16 months ago by
komal.rathi • 3.3k
Latest awards to komal.rathi
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For Batch query obsolete gene names to get current HGNC symbol
Appreciated
3 months ago,
created a post with more than 5 votes.
For C: DEXSeq with cufflinks gtf file
Popular Question
4 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Popular Question
4 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For C: have difficults using htseq count
Popular Question
5 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Epic Question
9 months ago,
created a question with more than 10,000 views.
For Bedtools Genomecoveragebed Usage : How To Create A Genome File?
Appreciated
9 months ago,
created a post with more than 5 votes.
For C: DEXSeq with cufflinks gtf file
Good Answer
9 months ago,
created an answer that was upvoted at least 5 times.
For A: Association between bed files - statistical significance
Popular Question
9 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Good Question
9 months ago,
asked a question that was upvoted at least 5 times.
For TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
Appreciated
9 months ago,
created a post with more than 5 votes.
For C: DEXSeq with cufflinks gtf file
Great Question
10 months ago,
created a question with more than 5,000 views.
For Bedtools Genomecoveragebed Usage : How To Create A Genome File?
Appreciated
10 months ago,
created a post with more than 5 votes.
For C: DEXSeq with cufflinks gtf file
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: Downloading ENCODE regulation data in .bed format by cell line
Appreciated
12 months ago,
created a post with more than 5 votes.
For A: Downloading ENCODE regulation data in .bed format by cell line
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Downloading ENCODE regulation data in .bed format by cell line
Great Question
14 months ago,
created a question with more than 5,000 views.
For TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Downloading ENCODE regulation data in .bed format by cell line
Great Question
16 months ago,
created a question with more than 5,000 views.
For TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Downloading ENCODE regulation data in .bed format by cell line
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: Downloading ENCODE regulation data in .bed format by cell line
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1860 users visited in the last hour