User: komal.rathi

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komal.rathi3.4k
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Children's Hospital of Philadelphia, Philadelphia, PA
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https://github.com/kom...
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2 days, 3 hours ago
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k**********@gmail.com

Posts by komal.rathi

<prev • 413 results • page 1 of 42 • next >
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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 3 months ago by komal.rathi3.4k
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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 3 months ago by komal.rathi3.4k
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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 3 months ago by komal.rathi3.4k
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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 7 months ago by komal.rathi3.4k
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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 9 months ago by komal.rathi3.4k
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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 12 months ago by komal.rathi3.4k
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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 12 months ago by komal.rathi3.4k • updated 12 months ago by Santosh Anand4.9k
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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 23 months ago by komal.rathi3.4k
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Comment: C: exon level quantification using htseq count
... 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.rathi3.4k
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Why does GFF prepared using dexseq_prepare_annotation shows different exon number than UCSC genome browser
... 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 ...
dexseq exons dexseq_prepare_annotation written 23 months ago by komal.rathi3.4k • updated 23 months ago by Devon Ryan91k

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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
Scholar 11 weeks ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
Popular Question 3 months ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Scholar 3 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
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
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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
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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
Scholar 9 months ago, created an answer that has been accepted. For A: cufflink and cuffmerge error
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

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