User: bioinfo8

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bioinfo870
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Posts by bioinfo8

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Answer: A: Tools To Calculate Average Coverage For A Bam File?
... Most answers seems to be very old and hence would like to have updated suggestions. I have 6 bam files and I have used `samtools depth` to calculate chromosome wise depth for all chromosomes and then plotted in R. While looking at the plots at 2-3 places, depth shows upto 200-3500 and hence I would ...
written 12 hours ago by bioinfo870
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Comment: C: Compute inner mate distance for paired-end reads in a bam file
... As per [Paired-end read confusion - library, fragment or insert size?][1], will it calculate inner mate distance distribution and not insert size distribution? [1]: http://thegenomefactory.blogspot.de/2013/08/paired-end-read-confusion-library.html ...
written 4 days ago by bioinfo870
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Comment: C: Compute inner mate distance for paired-end reads in a bam file
... I am interested to compute all parameters and alignment statistics for my aligned bam files ([Whole exomes: comparative analysis][1] ) and one of them was inner mate distance between paired reads. I was looking for the explanation of histogram and came across with the linked post. I assume FR=forwar ...
written 4 days ago by bioinfo870
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Comment: C: Calculating inner mate distance for paired reads
... Done. Here it is: [Compute inner mate distance for paired-end reads in a bam file][1] [1]: https://www.biostars.org/p/259454/ ...
written 4 days ago by bioinfo870
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Compute inner mate distance for paired-end reads in a bam file
... Hi, I am interested to calculate inner mate distance for paired-end reads in many bam files i.e. distance from the right-most end of the left read to the left-most end of the right read and all the properly paired QC-passed reads that map in the bam file (ref: [Calculating inner mate distance for p ...
paired picard bam written 4 days ago by bioinfo870 • updated 4 days ago by Devon Ryan68k
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Answer: A: Calculating inner mate distance for paired reads
... I have used CollectInsertSizeMetrics.jar (ref: [Picard MarkDuplicates error after using bamaddrg: "bin field of BAM record does not equal value computed..."][1] ) and got the attached insert size histogram for my bam file (which includes properly-paired QC-passed reads, sorted and indexed). However, ...
written 4 days ago by bioinfo870
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Comment: C: Calculating inner mate distance for paired reads
... Is there any way in samtools to do this? Thanks. ...
written 5 days ago by bioinfo870
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Comment: C: How to plot coverage and depth statistics of a bam file
... Would you guide how to plot same chromosome in one graph from multiple samples (bam) files? Thanks. ...
written 7 days ago by bioinfo870
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Comment: C: How to plot coverage and depth statistics of a bam file
... Ok. I have exome bam files of different individuals from same organism. ...
written 7 days ago by bioinfo870
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Comment: C: How to plot coverage and depth statistics of a bam file
... Thanks Vivek. I have gone through various posts but still unclear whether to use `samtools depth` or `samtools mpileup` to calculate coverage of my multiple bam files. Secondly, as each file is very big, I am thinking to plot different chromosomes from multiple bam files in multiple plots, for e.g. ...
written 7 days ago by bioinfo870

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