User: Diploid Progenitor

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10
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New User
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Last seen:
1 year ago
Joined:
2 years, 5 months ago
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h*********@hotmail.de

I came here from Biostars Galaxy, is this an upgrade or a downgrade?

Posts by Diploid Progenitor

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Formula for extracting per base read depth/per base genome coverage from a SAM f
... Hi, I haven't tried SAMtools, but have been using bedtools `genomecov`, which works for me. I am simply curious as to how these tools extract the relevant information from the BAM/SAM format, and if there is a straightforward formula that they use to do so. ...
written 2.0 years ago by Diploid Progenitor10
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Comment: C: Formula for extracting per base read depth/per base genome coverage from a SAM f
... Hello Devon, Thank you for your response. I am currently using bedtools and it is working just fine. I was just curious as to how this tool and SAMtools extract the relevant information from the BAM/SAM format, i.e. if there is a straightforward formula being applied here could easily be emulated. ...
written 2.0 years ago by Diploid Progenitor10
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Formula for extracting per base read depth/per base genome coverage from a SAM file?
... Hello, Is anyone aware of a way to extract per base read depth/per base genome coverage directly from a SAM file without making use of applications such as bedtools or SAMtools? As in, which columns in the SAM file contain the relevant information required to calculate per base read depth, and ho ...
bedtools alignment samtools sam coverage written 2.0 years ago by Diploid Progenitor10 • updated 2.0 years ago by Devon Ryan95k
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Comment: C: Are there maximum gap penalty scores in BWA-MEM?
... Hello Macspider, Thank you for your response. I guess there is no maximum penalty score, so I would probably be safe setting the penalty value to something ridiculously high, like 100, while keeping the default X-dropoff value (-d), so that the seed extension will stop as soon as a gap is encounter ...
written 2.5 years ago by Diploid Progenitor10
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Comment: C: RNA_seq Data analysis Help - Uneven coverage of reads across gene!
... Hello, There are a bunch of tools in Galaxy such as MarkDuplicates and RmDup that can be used for the identification and removal of duplicate reads if you want to use your data for things like variant calling. ...
written 2.5 years ago by Diploid Progenitor10
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Are there maximum gap penalty scores in BWA-MEM?
... Apologies if this is a simplistic question. I originally asked this in the Galaxy Biostars channel but there was no answer, so I thought I'd try my luck here. I am working on a variant calling workflow for paired DNAseq reads, with BWA-MEM as my aligner. To achieve high confidence when aligning to ...
bwa-mem alignment written 2.5 years ago by Diploid Progenitor10 • updated 2.5 years ago by Macspider3.0k

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Supporter 2.5 years ago, voted at least 25 times.

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