User: komal.rathi
komal.rathi • 3.5k
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- Children's Hospital of Philadelphia, Philadelphia, PA
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- Joined:
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Posts by komal.rathi
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... What versions of STAR/RSEM are you using?
Also, can you do a `tree` (or show the directory structure) on your working directory? I see you have hardcoded the paths of `bam/, fastq/ and quant/`. Just want to make sure these directories exist. ...
written 5 months ago by
komal.rathi • 3.5k
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... Can you move this to an answer so I can accept it? Thanks! ...
written 6 months ago by
komal.rathi • 3.5k
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... 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 10 months ago by
komal.rathi • 3.5k
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... Thanks, I will do that. I will keep this open and post any responses I get from the help desk. ...
written 10 months ago by
komal.rathi • 3.5k
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... 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 10 months ago by
komal.rathi • 3.5k
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... I ended up doing a chisq test using the output of ASEReadCounter. ...
written 14 months ago by
komal.rathi • 3.5k
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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 17 months ago by
komal.rathi • 3.5k
0
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530
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... 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 19 months ago by
komal.rathi • 3.5k
0
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... 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 19 months ago by
komal.rathi • 3.5k
• updated
19 months ago by
Santosh Anand ♦ 5.0k
0
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1.0k
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... Thank you very much for the explanation!! ...
written 2.5 years ago by
komal.rathi • 3.5k
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