User: lstbl

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lstbl40
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Posts by lstbl

<prev • 8 results • page 1 of 1 • next >
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confusion about BCFtools "EXPRESSIONS" flags
... I'm hoping someone can help me understand the "EXPRESSIONS" flags used in bfctools. I'm trying to filter variants from a vcf file produced using the 'mpileup' program from samtools. Essentially, I want to perform a simple filtering step that will exclude all reads that don't pass a threshold (say, ...
bfctools samtools mpileup written 8 months ago by lstbl40
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explaination of NCBIs spot descriptor
... I'm very confused by NCBI's spot descriptor language, I'm hoping someone on here has some insight. For example, if we look at this entry: http://www.ncbi.nlm.nih.gov/sra/SRX849019, the spot descriptor says forward 1 reverse 152. Does this mean that, when you dump the file (using fastq-dump without ...
ncbi sra spot descriptor written 9 months ago by lstbl40
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Answer: A: Meaning of "%" in expressions for bcftools filter
... This is because when you include a `%` inside of quotes, it will act as a stdin for the program. See this post: http://serverfault.com/questions/274475/escaping-double-quotes-and-percent-signs-in-cron ...
written 9 months ago by lstbl40
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Comment: C: whole genome capillary shotgun reads to call SNPs
... Hi John, one more question if you could spare the time. Looking at samtools mpileup, I can't seem to figure out how to set the sensitivity based on 'number of reads that support' a SNP. The only thing I see is a -m flag (minimum number of reads for indel candidates). However, there doesn't seem to ...
written 9 months ago by lstbl40
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Comment: C: whole genome capillary shotgun reads to call SNPs
... Wow, what a great reply. I wish I could give you more than just one upvote for that. Thanks for taking the time to answer my questions about this. I definitely understand the subtleties of BQSR and SNP calling in general much better after reading your comments. ...
written 9 months ago by lstbl40
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Comment: C: whole genome capillary shotgun reads to call SNPs
... Hi John, Thanks for your reply. Do you have an example of a "simple" SNP caller that you mentioned above, or would you just write a very simple one using some heuristics (e.g. call a SNP if it doesn't violate a binomial distribution with p=0.5)? I think I could do that fairly easily with python usi ...
written 9 months ago by lstbl40
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whole genome capillary shotgun reads to call SNPs
... I'm currently trying to use the GATK pipeline for SNP calling to call SNPs. At the step where you use GATK's 'BaseRecalibrator' tool, you have to provide a set of known SNPs. Unfortunately, for my organisms, these are not annotated. However, these organisms do have a reference genome sequenced. In ...
snp sequencing written 9 months ago by lstbl40 • updated 9 months ago by John10k
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preprocessing genome fasta file prior to mapping?
... Hi Everyone, Sorry if this is a dup, but I can't seem to find a satisfactory answer on this site or others. I'm wondering what, if any, pre-processing I should perform on a reference genome fasta/gff file prior to mapping using BWA or Bowtie. For example, if I wanted to map something to the [orang ...
next-gen bwa bowtie sequencing written 9 months ago by lstbl40

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