User: komal.rathi

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komal.rathi3.5k
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Location:
Children's Hospital of Philadelphia, Philadelphia, PA
Website:
https://github.com/kom...
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komalsrathi
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3 weeks, 4 days ago
Joined:
6 years, 11 months ago
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Posts by komal.rathi

<prev • 415 results • page 1 of 42 • next >
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Comment: C: snakemake: pipeline failed with MissingOutputException
... 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.rathi3.5k
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Comment: C: Download all eQTL data for all the 9 tissues from GTEx Portal
... Can you move this to an answer so I can accept it? Thanks! ...
written 6 months ago by komal.rathi3.5k
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Answer: A: How to get known canonical transcript information from UCSC for a specific genco
... 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.rathi3.5k
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Comment: C: How to get known canonical transcript information from UCSC for a specific genco
... 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.rathi3.5k
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How to get known canonical transcript information from UCSC for a specific gencode version
... 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 ...
gencode canonical transcripts ucsc written 10 months ago by komal.rathi3.5k
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Comment: C: GATK ASEReadCounter: Downstream analysis for identifying allele specific express
... I ended up doing a chisq test using the output of ASEReadCounter. ...
written 14 months ago by komal.rathi3.5k
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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.rathi3.5k
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Comment: C: How to determine RNA-seq samples from dbGaP metadata
... 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.rathi3.5k
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How to determine RNA-seq samples from dbGaP metadata
... 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 ...
metadata dbgap written 19 months ago by komal.rathi3.5k • updated 19 months ago by Santosh Anand5.0k
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Comment: C: Why does GFF prepared using dexseq_prepare_annotation shows different exon numbe
... Thank you very much for the explanation!! ...
written 2.5 years ago by komal.rathi3.5k

Latest awards to komal.rathi

Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: have difficults using htseq count
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: How the best way to verify the up and down regulated genes in a list of DE genes
Teacher 12 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
Appreciated 5 months ago, created a post with more than 5 votes. For C: DEXSeq with cufflinks gtf file
Scholar 5 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
Great Question 5 months ago, created a question with more than 5,000 views. For How To Get Mapping Statistics On Bam File
Scholar 5 months ago, created an answer that has been accepted. For A: Error in htseq-count: "Malformed SAM line: MRNM == '*' although flag bit &0x0008
Popular Question 7 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Popular Question 7 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 8 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: have difficults using htseq count
Scholar 10 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
Popular Question 10 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Scholar 10 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: have difficults using htseq count
Popular Question 11 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Association between bed files - statistical significance
Popular Question 13 months ago, created a question with more than 1,000 views. For How to find Significant Trans- Interactions in HiC data
Popular Question 13 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 13 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Popular Question 13 months ago, created a question with more than 1,000 views. For Identify genes with extracellular matrix domains
Appreciated 13 months ago, created a post with more than 5 votes. For C: DEXSeq with cufflinks gtf file
Great Question 13 months ago, created a question with more than 5,000 views. For Download all eQTL data for all the 9 tissues from GTEx Portal

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