User: b10hazard

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b10hazard20
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New User
Location:
United States
Last seen:
2 months, 2 weeks ago
Joined:
3 years, 11 months ago
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Posts by b10hazard

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How do I get the read counts for a specific exon
... Yup, the file is populated with repeats of what you posted above. I've given up on htseq-count. I used samtools depth to get my answer. I have no idea what is up with htseq-count. Could be some config/package dependency bug on our cluster. ...
written 11 weeks ago by b10hazard20
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Comment: C: How do I get the read counts for a specific exon
... Yes, initially I was trying the tool on the entire bam thinking that the tools would use the provided GTF or BED files to target the specified exon instead of parsing **the entire file**. Why the heck these tools parse the entire file when the user specifies a targeted region is beyond me. Then I ...
written 11 weeks ago by b10hazard20
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Comment: C: How do I get the read counts for a specific exon
... Already tried that. The output of htseq-count and bedtools coverage is smaller but it doesn't solve the fundamental problem of the output file being exon specific. I'm trying dexseq right now. Hopefully that tool won't produce gibberish. ...
written 11 weeks ago by b10hazard20
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Comment: C: How do I get the read counts for a specific exon
... Of course I did. The gazillion answers I found all sucked. I tried bedtools coverage via... > bedtools coverage -abam mybam.bam -b mygtf.bed > results_bedtools.txt But just got a 8.6 GB file containing a ton of useless info an none of it was grouped by exon. Then I tried... > htseq-co ...
written 11 weeks ago by b10hazard20
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How do I get the read counts for a specific exon
... I have a bam file and a gtf file that contains a single line.... chr5 UCSC exon 13744354 13744380 . + . gene_id "UDHG"; transcript_id "NM_033847"; gene_name "UDHG"; The bam file contains paired end reads. How do I get the number of reads that align ...
bam exon written 11 weeks ago by b10hazard20 • updated 11 weeks ago by Ram15k
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allele depth and depth do not match in my vcf file
... I have vcf file where the allele depth and depth do not match. Why is this? Here is the offending line.... > chrX 155252833 . G . 81 . DP=12;AD=10;MQSB=0.183296;MQ0F=0.333333;AN=2;DP4=7,3,0,0;MQ=6 GT 0/0 DP is the depth, right? In this example DP is 12. So how come AD is 10? ...
vcf written 3 months ago by b10hazard20 • updated 3 months ago by Pierre Lindenbaum108k
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how would I find SNPs that are highly polymorphic between populations in dbSNP
... Hi there, I’m trying to get a vcd file containing SNPs that are highly polymorphic by population. Does anything like this exist in dbSNP? I’m guessing I would want to find SNPs with [high fixation indexes][1] between populations but I have no idea how to do this. Any advice would be great. Than ...
ncbi allele dbsnp snp written 3 months ago by b10hazard20 • updated 3 months ago by agata88660
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Comment: C: how do I get a vcf containing germline snps from dbSNP?
... One more question. Are there redunant entries in dbSNP? I was trying to parse the common_no_known_medical_impact_20170905.vcf.gz file I downloaded from the links you posted but in this file there are about 38 million entries. dbSNP is only supposed to have 13 million, right? ...
written 3 months ago by b10hazard20
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Comment: C: how do I get a vcf containing germline snps from dbSNP?
... Excellent! Thanks for the links and the wonderful explanation! ...
written 3 months ago by b10hazard20
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how do I get a vcf containing germline snps from dbSNP?
... I'm trying to get a VCF file containing germline SNPs from NCBI's databases. [This page][1] says that I want the common_no_known_medical_impact.vcf.gz file and that I can find it at... ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF/ However that section only lists the common_a ...
ncbi vcf dbsnp written 3 months ago by b10hazard20 • updated 3 months ago by Kevin Blighe21k

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