User: mplace

gravatar for mplace
mplace40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
7 months, 4 weeks ago
Joined:
4 years, 10 months ago
Email:
m*****@wisc.edu

Posts by mplace

<prev • 10 results • page 1 of 1 • next >
3
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Answer: A: Splitting A Vcf File
... I know this is an old post, but this method modified from above, (Jorge ) is much faster. Get list of sample names: for sample in `bcftools view -h MyData.vcf.gz | grep "^#CHROM" | cut -f10-`; do echo $sample; done > sampleNames.txt split vcf files faster: parallel -a sampleName ...
written 2.1 years ago by mplace40 • updated 2.1 years ago by WouterDeCoster42k
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Comment: C: Merge SNP & INDEL vcf files
... Thank you for the help. ...
written 2.7 years ago by mplace40
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Comment: A: Merge SNP & INDEL vcf files
... The PI I work for would like to be able to generate strain specific gene sequences which include both snps and indels for the generation of PCR primers etc... What happens when I combine the snp and indel vcf and there are overlapping sites? ...
written 2.7 years ago by mplace40
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Merge SNP & INDEL vcf files
... I am creating a gene sequence for a sample in the vcf using a standard reference genome. The command for generating the sequence I found on this site works well. samtools faidx ref.fasta chrom:start-stop | bcftools consensus -s sample my.vcf But I have separate SNP and INDEL vcf files generated us ...
vcf indel snp written 2.7 years ago by mplace40
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Answer: A: Python multiprocessing FASTQ file
... Thanks for all the information, very helpful ...
written 3.8 years ago by mplace40
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Answer: A: Python multiprocessing FASTQ file
... The dict change result in a 10-fold increase in speed, very nice thanks again ...
written 3.8 years ago by mplace40
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Answer: A: Python multiprocessing FASTQ file
... Makes sense,  I will make the changes to use  "if key in dict:",  if that is too slow I will switch to c++. Thank you for taking the time to comment.     ...
written 3.8 years ago by mplace40
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Python multiprocessing FASTQ file
... I have a large fastq file, ~40GB of short 50bp illumina reads.   The first 10bp are an experiment identifer tag, 18bp follow that are the same for all reads, the remainder of the sequence is the first 22 bp of a gene.  I have a script which identifies the experiment and the gene given a "decode" fil ...
multiprocessing python fastq written 3.8 years ago by mplace40
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Answer: A: Manipulating/Extracting Data and Developing Methods - Language Choice
... Bash  - nice easy loops on command line Perl - also great on the command line sed, awk for one-liners for pasting files, and quick substitutions Python for code  you must pass on to others, It can be a real pain reading someone else's perl code. R for plotting   ...
written 4.2 years ago by mplace40
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snpeff Warnings , transcript incomplete
... I am having a hard time deciphering the real meaning of the warnings issued by snpeff. snpeff docs state: WARNING_TRANSCRIPT_INCOMPLETE    -- A protein coding transcript having a non-multiple of 3 length. It indicates that the reference genome has missing information about this particular transcri ...
snpeff written 4.8 years ago by mplace40 • updated 4.8 years ago by RT340

Latest awards to mplace

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Splitting A Vcf File
Popular Question 23 months ago, created a question with more than 1,000 views. For Python multiprocessing FASTQ file
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Python multiprocessing FASTQ file
Popular Question 3.0 years ago, created a question with more than 1,000 views. For snpeff Warnings , transcript incomplete

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