User: Varun Gupta
Varun Gupta • 1000
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Posts by Varun Gupta
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Comment:
C: Picard Mark Duplicates
... Does picard takes soft clipped bases into account then? ...
written 5 weeks ago by
Varun Gupta • 1000
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Comment:
C: Picard Mark Duplicates
... Hi finswimmer,
I tried the same thing with samtools rmdup and it considers them as duplicates and retains the one with high mapping quality. Regarding the soft clip bases, I don't think soft clipped bases has to do with this thing because the position 88015806 in the above example is the position st ...
written 5 weeks ago by
Varun Gupta • 1000
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Comment:
C: Picard Mark Duplicates
... Thanks Pierre. Can we provide a list of Barcodes and not 1 BARCODE sequence to BARCODE_TAG option? The library was indeed created with Unique Molecular Barcodes(96 of them) ...
written 5 weeks ago by
Varun Gupta • 1000
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... Hi,
I have used Picard MarkDuplicates tool to remove duplicates from my bam file. Understanding it correctly, if there are more than 1 reads starting at the same position, then after removing for duplicates, only 1 read will be present in the bam file generated from MARKDUPLICATES based on its qual ...
written 5 weeks ago by
Varun Gupta • 1000
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... yup, works fine, must say better than genomeCoverageBed because in genomeCoverageBed, if you have all the headers(having all the chromosomes) in the bam file and only a particular chr alignments you want, it still goes through all the chromosomes.
...
written 7 weeks ago by
Varun Gupta • 1000
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... Hi Kevin,
Thanks for your reply. I looked at the bedtools manual for coverage function. If I want per nucleotide coverage for the bed file(as is my case), the command should be like this
bedtools coverage -a mygenes.bed -b test.bam -d
Then this is the output
chr5 10000 23456 10001 14
...
written 7 weeks ago by
Varun Gupta • 1000
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5 follow
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... Hello,
I want to get per nucleotide coverage for my particular gene (geneX) which I added in the fasta file. There are other chromosomes present in the bam file, whose per nu coverage I am not interested in. When I use genomeCoverageBed tool to calculate per nucleotide coverage for my gene I also g ...
written 7 weeks ago by
Varun Gupta • 1000
• updated
7 weeks ago by
Kevin Blighe ♦ 19k
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... ![enter image description here][1]Hi Venu,
I tried making plots by providing this command
./pyGenomeTracks --tracks tracks.ini --BED ~/test.bed -out fig_
The graph is showing too much upstream and downstream of my bed coordinates. Any way to fix that
Also how can i display the name of the feat ...
written 3 months ago by
Varun Gupta • 1000
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... It got installed here
/home/varun/.local/bin ...
written 3 months ago by
Varun Gupta • 1000
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362
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... pip install pyGenomeTracks ...
written 3 months ago by
Varun Gupta • 1000
Latest awards to Varun Gupta
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For Removing low quality ends from a fastq file
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For Homologous Genes In Mouse For Given Human Genes
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For RNA Seq datasets for different tissues not Poly-A selected
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For Tophat Junctions.Bed File
Teacher
5 months ago,
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For A: Help With Perl Script: Store Fasta Sequences Into A Hash.
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8 months ago,
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For RNA Seq datasets for different tissues not Poly-A selected
Teacher
8 months ago,
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For A: Help With Perl Script: Store Fasta Sequences Into A Hash.
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For Yeast genome SK1 strain
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For Tophat Junctions.Bed File
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9 months ago,
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For Homologous Genes In Mouse For Given Human Genes
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For Homologous Genes In Mouse For Given Human Genes
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For Homologous Genes In Mouse For Given Human Genes
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For Homologous Genes In Mouse For Given Human Genes
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14 months ago,
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For Tophat Junctions Bed File Strand Column
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