User: cmo

gravatar for cmo
cmo30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
3 days, 1 hour ago
Joined:
2 years, 3 months ago
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c********@gmail.com

Posts by cmo

<prev • 11 results • page 1 of 2 • next >
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Answer: A: tool to change flag for all reads in a bam file
... Indeed Heng Li's BioAwk does the job nicely: samtools view -H out.sam > header samtools view out.sam | \ bioawk -c sam '{ $flag = and($flag , 3860 ) ; print $0 }' | \ cat header - > new.sam Note that "3860" is the flag which sets all bits associate ...
written 3 months ago by cmo30
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Comment: C: tool to change flag for all reads in a bam file
... updated to include GEM commands ...
written 3 months ago by cmo30
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tool to change flag for all reads in a bam file
... Is there a tool which will edit the flag for all reads in a BAM file? In my case: The GEM aligner sets the "paired" flag for all reads in the resulting BAM file.... even if you give it single-ended reads. This causes PICARD, GATK, etc. to throw many Warnings or Exit. Thus, I need a tool that will ...
bam sam written 3 months ago by cmo30
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gatk base recalibration results for 1000 genomes
... I'd bet good money that somebody, probably at Broad Institute, has ran GATK's [BQSR][1] base quality score recalibration) on all of the BAM files for 1000 Genomes (and probably TCGA, etc.) and saved the recalibration table output files somewhere. Does anybody know if all of the base recalibration ...
indel 1000 genomes snp gatk written 5 months ago by cmo30 • updated 4 months ago by Biostar ♦♦ 10
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List of genome sequencing projects
... I am looking for a list of large-scale Illumina-based **whole genome** sequencing projects of many individuals. Human or otherwise (but preferably higher eukaryotes). Here are the few that I know of: 1. 1000 Genomes Project (~2500 humans, worldwide) 2. TCGA - The Cancer Genome Atlas (tumor &am ...
genome illumina ngs dna-seq sequencing written 5 months ago by cmo30
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report all possible alignments
... I am not interested in read mapping per se. I am interested in reporting ALL possible end-to-end alignments of a read against a reference that have <= k mismatches (e.g. k = 5).  I do not care about the "best" alignment. Standard DNA & RNA read aligners (bwa, bowtie, STAR, etc.) that try to ...
multimapping alignment written 19 months ago by cmo30 • updated 19 months ago by h.mon4.5k
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Comment: C: bwa mem failed to allocate memory
... Good point Devon.  Yes, i allocated the whole node, so it is all mine. ...
written 2.1 years ago by cmo30
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bwa mem failed to allocate memory
... I am aligning a modest number of short reads (10.5 M) to a large genome (~4 Gb) with bwa mem .  I expect a high error rate and expect many multiply mapping reads, so I relax some of the parameters as follows: bwa mem  -t 32 -k 15  -r 1.25  -c 100000000  -B 1  -O 0  -E 1  -L 500  -T 12 I keep gett ...
bwa-mem allocate memory bwa written 2.1 years ago by cmo30
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Comment: C: aligner for CORRECTED pacbio long reads
... Thank you, but I am more interested in how to align after the PacBio long reads are corrected.  I am not necessarily interested in a de-novo assembly.  And the correction step should be taken as given, I am not interested in correction methods. ...
written 2.1 years ago by cmo30
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aligner for CORRECTED pacbio long reads
... After error-correcting PacBio long reads using Illumina short-reads, what aligners are adept for aligning the corrected PacBio long reads against the genome? Should I think of the corrected PacBio reads as just "long Illumina reads" (in terms of error & indel rate, etc.) ? I am tempted to use ...
reads pacbio align longreads sequencing written 2.1 years ago by cmo30 • updated 6 weeks ago by Felix Francis340

Latest awards to cmo

Scholar 3 months ago, created an answer that has been accepted. For A: tool to change flag for all reads in a bam file
Popular Question 9 months ago, created a question with more than 1,000 views. For aligner for CORRECTED pacbio long reads
Popular Question 11 months ago, created a question with more than 1,000 views. For bwa mem failed to allocate memory
Voter 13 months ago, voted more than 100 times.
Supporter 2.1 years ago, voted at least 25 times.

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