User: komal.rathi
komal.rathi • 3.4k
- Reputation:
- 3,440
- Status:
- Trusted
- Location:
- Children's Hospital of Philadelphia, Philadelphia, PA
- Website:
- https://github.com/kom...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 days, 3 hours ago
- Joined:
- 6 years, 4 months ago
- Email:
- k**********@gmail.com
Posts by komal.rathi
<prev
• 413 results •
page 1 of 42 •
next >
2
votes
1
answer
247
views
1
answers
... I got a response from the UCSC Genome Browser help desk which resolved my question:
> The knownCanonical gene set is created from the longest transcript of
> the basic Gencode gene set. This convention was not around for the V23
> gene set, so that file does not exist. If you would like to ...
written 3 months ago by
komal.rathi • 3.4k
1
vote
1
answer
247
views
1
answers
... Thanks, I will do that. I will keep this open and post any responses I get from the help desk. ...
written 3 months ago by
komal.rathi • 3.4k
3
votes
1
answer
247
views
1
answer
... Hi,
I am using UCSC genome browser to get known canonical transcripts using this [link][1]. This is the default Gencode version V29 and I am able to set the `table` to `knownCanonical`. However, when I change the gencode version to `ALL Gencode V23` under `track`, the table options change and I can ...
written 3 months ago by
komal.rathi • 3.4k
0
votes
2
answers
1.9k
views
2
answers
... I ended up doing a chisq test using the output of ASEReadCounter. ...
written 7 months ago by
komal.rathi • 3.4k
0
votes
0
answers
1.2k
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 9 months ago by
komal.rathi • 3.4k
0
votes
1
answer
396
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 12 months ago by
komal.rathi • 3.4k
0
votes
1
answer
396
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 12 months ago by
komal.rathi • 3.4k
• updated
12 months ago by
Santosh Anand ♦ 4.9k
0
votes
1
answer
806
views
1
answers
... Thank you very much for the explanation!! ...
written 23 months ago by
komal.rathi • 3.4k
0
votes
1
answer
1.5k
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 23 months ago by
komal.rathi • 3.4k
5
votes
1
answer
806
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 23 months ago by
komal.rathi • 3.4k
• updated
23 months ago by
Devon Ryan ♦ 91k
Latest awards to komal.rathi
Popular Question
18 days ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For C: have difficults using htseq count
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For C: have difficults using htseq count
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Good Answer
5 months ago,
created an answer that was upvoted at least 5 times.
For A: Association between bed files - statistical significance
Popular Question
5 months ago,
created a question with more than 1,000 views.
For How to find Significant Trans- Interactions in HiC data
Popular Question
5 months ago,
created a question with more than 1,000 views.
For DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
Popular Question
5 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Identify genes with extracellular matrix domains
Appreciated
6 months ago,
created a post with more than 5 votes.
For C: DEXSeq with cufflinks gtf file
Great Question
6 months ago,
created a question with more than 5,000 views.
For Download all eQTL data for all the 9 tissues from GTEx Portal
Great Question
6 months ago,
created a question with more than 5,000 views.
For How To Get Mapping Statistics On Bam File
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Batch query obsolete gene names to get current HGNC symbol
Popular Question
9 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Appreciated
10 months ago,
created a post with more than 5 votes.
For C: DEXSeq with cufflinks gtf file
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For C: have difficults using htseq count
Popular Question
12 months ago,
created a question with more than 1,000 views.
For How to sort fastq.gz files efficiently
Good Answer
16 months ago,
created an answer that was upvoted at least 5 times.
For A: Association between bed files - statistical significance
Appreciated
16 months ago,
created a post with more than 5 votes.
For C: DEXSeq with cufflinks gtf file
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1399 users visited in the last hour