User: Varun Gupta
Varun Gupta • 1.1k
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Posts by Varun Gupta
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... Hi,
I want to filter my fastq reads based on ambiguous characters, basically **N's**. So if I have a read sequence having N's greater than 5%, I want to discard that read, if lower than 5%, I want to keep it. It would be really helpful if someone know about any tool which already does that.
Thanks ...
written 19 months ago by
Varun Gupta • 1.1k
• updated
19 months ago by
Pierre Lindenbaum ♦ 125k
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Comment:
C: Picard Mark Duplicates
... Does picard takes soft clipped bases into account then? ...
written 21 months ago by
Varun Gupta • 1.1k
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2.3k
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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 21 months ago by
Varun Gupta • 1.1k
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2.3k
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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 21 months ago by
Varun Gupta • 1.1k
2
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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 21 months ago by
Varun Gupta • 1.1k
• updated
20 months ago by
marcela.uliano • 60
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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 22 months ago by
Varun Gupta • 1.1k
0
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1.1k
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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 22 months ago by
Varun Gupta • 1.1k
6
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6 follow
1
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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 22 months ago by
Varun Gupta • 1.1k
• updated
22 months ago by
Kevin Blighe ♦ 53k
0
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4
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1.2k
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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 24 months ago by
Varun Gupta • 1.1k
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4
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1.2k
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... It got installed here
/home/varun/.local/bin ...
written 24 months ago by
Varun Gupta • 1.1k
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