User: komal.rathi

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komal.rathi3.2k
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Children's Hospital of Philadelphia, Philadelphia, PA
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https://github.com/kom...
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Posts by komal.rathi

<prev • 408 results • page 1 of 41 • next >
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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 5 weeks ago by komal.rathi3.2k
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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 5 weeks ago by komal.rathi3.2k • updated 5 weeks ago by Santosh Anand3.9k
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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 12 months ago by komal.rathi3.2k
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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 12 months ago by komal.rathi3.2k
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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 12 months ago by komal.rathi3.2k • updated 12 months ago by Devon Ryan84k
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Comment: C: Filter bam files using a bed file: Why is the mate missing?
... Thanks I just thought it would be simpler than this. I was hoping something like a partial match would work.. ...
written 12 months ago by komal.rathi3.2k
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Filter bam files using a bed file: Why is the mate missing?
... 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 ...
samtools rna-seq written 12 months ago by komal.rathi3.2k
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Comment: C: exon level quantification using htseq count
... 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 12 months ago by komal.rathi3.2k
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Comment: C: exon level quantification using htseq count
... Hi Devon, thanks for the suggestion. I used python dexseq_prepare_annotation.py gencode.v23.annotation_subset.gtf gencode.v23.annotation_subset.gff and this is how the gff looks: chr1 dexseq_prepare_annotation.py aggregate_gene 229431245 229434098 . - . gene_id "ENSG00000143632.14" ...
written 12 months ago by komal.rathi3.2k
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exon level quantification using htseq count
... Hi everyone, This is my htseq-count command for gene level counts: htseq-count -f bam -r name -s yes -a 10 -t exon -i gene_id -m union sample_Aligned.out.bam gencode.v23.annotation_subset.gtf > sample_Aligned.out.table.txt ENSG00000075624.13 171006 ENSG00000107554.15 379 ENSG00 ...
htseq-count exon quantifications rna-seq written 12 months ago by komal.rathi3.2k • updated 12 months ago by Devon Ryan84k

Latest awards to komal.rathi

Popular Question 8 days ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Teacher 8 days ago, created an answer with at least 3 up-votes. For C: have difficults using htseq count
Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to sort fastq.gz files efficiently
Epic Question 5 months ago, created a question with more than 10,000 views. For Bedtools Genomecoveragebed Usage : How To Create A Genome File?
Appreciated 5 months ago, created a post with more than 5 votes. For C: DEXSeq with cufflinks gtf file
Popular Question 5 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
Good Question 5 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 5 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 Bedtools Genomecoveragebed Usage : How To Create A Genome File?
Appreciated 6 months ago, created a post with more than 5 votes. For C: DEXSeq with cufflinks gtf file
Good Answer 7 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 8 months ago, created a post with more than 5 votes. For A: Downloading ENCODE regulation data in .bed format by cell line
Teacher 10 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 10 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 10 months ago, created an answer with at least 3 up-votes. For A: Downloading ENCODE regulation data in .bed format by cell line
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Loading plot with R
Great Question 12 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 12 months ago, created an answer with at least 3 up-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
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
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Downloading ENCODE regulation data in .bed format by cell line
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Downloading ENCODE regulation data in .bed format by cell line
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Epic Question 16 months ago, created a question with more than 10,000 views. For How To Get Mapping Statistics On Bam File

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