User: cmo

gravatar for cmo
cmo60
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60
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7 hours ago
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4 years, 12 months ago
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Posts by cmo

<prev • 18 results • page 1 of 2 • next >
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How to turn off Quality score binning in bcl2fastq
... Newer versions of bcl2fastq automatically bin the quality scores into just a few values. For example, for much of the recently-produced data I have worked with, all of the quality scores are one of: Q2, Q11, Q25, or Q37. The command line help for bcl2fastq does not list any option to disable the b ...
illumina ngs written 7 hours ago by cmo60
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Answer: A: map refseq to identical genbank
... This information is in the /ASSEMBLY_REPORTS/ directory on the Genomes FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/ I contacted NCBI, and NLM Support (nlm-support@nlm.nih.gov) provided the following answer: > As you will learn in the README file, columns 18 and 19 in the > ...
written 4 weeks ago by cmo60
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Comment: C: map refseq to identical genbank
... yes, i imagined the relationship is encoded somewhere. interesting idea, though. ...
written 6 weeks ago by cmo60
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Comment: C: map refseq to identical genbank
... good idea, but this will not scale to thousands of accessions, as indicated in the question. ...
written 6 weeks ago by cmo60
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Comment: C: map refseq to identical genbank
... good idea, but this will not scale to thousands of accessions, as indicated in the question. ...
written 6 weeks ago by cmo60
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map refseq to identical genbank
... Some databases provide Genbank coordinates. Others provide RefSeq coordinates. I am looking for a table of pairwise associations between identical Genbank and Refseq records. The ultimate goal is: if I have e.g. a BED file with tens of thousands of annotations across thousands of Genbank genomes, ...
ncbi assembly refseq genbank written 6 weeks ago by cmo60
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RNA secondary structure interactive visualization with save
... - I have a complicated secondary structure for a very large RNA (1kb) that I want to visualize. - I need to be able to interactively/manually edit the visualization according to my liking. - I also need to color certain residues. - I also would like to save the visualization for later use. Doe ...
rna visualization written 20 months ago by cmo60
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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 3.0 years ago by cmo60
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Comment: C: tool to change flag for all reads in a bam file
... updated to include GEM commands ...
written 3.0 years ago by cmo60
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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 3.0 years ago by cmo60

Latest awards to cmo

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: map refseq to identical genbank
Scholar 4 weeks ago, created an answer that has been accepted. For A: tool to change flag for all reads in a bam file
Popular Question 7 weeks ago, created a question with more than 1,000 views. For aligner for CORRECTED pacbio long reads
Popular Question 14 months ago, created a question with more than 1,000 views. For aligner for CORRECTED pacbio long reads
Popular Question 19 months ago, created a question with more than 1,000 views. For List of genome sequencing projects
Popular Question 2.2 years ago, created a question with more than 1,000 views. For List of genome sequencing projects
Popular Question 2.6 years ago, created a question with more than 1,000 views. For bwa mem failed to allocate memory
Scholar 3.0 years ago, created an answer that has been accepted. For A: tool to change flag for all reads in a bam file
Popular Question 3.5 years ago, created a question with more than 1,000 views. For aligner for CORRECTED pacbio long reads
Popular Question 3.7 years ago, created a question with more than 1,000 views. For bwa mem failed to allocate memory
Voter 3.8 years ago, voted more than 100 times.
Supporter 4.8 years ago, voted at least 25 times.

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