User: hafiz.talhamalik

Reputation:
230
Status:
Trusted
Location:
Pakistan
Twitter:
@hafizmuhdtalha
Last seen:
3 days ago
Joined:
4 years, 2 months ago
Email:
h***************@gmail.com

Posts by hafiz.talhamalik

<prev • 106 results • page 1 of 11 • next >
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Comment: C: EdgeR Warning message In estimateCommonDisp.
... what's in ur expt variable ?? how many replicates ?? ...
written 7 days ago by hafiz.talhamalik230
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Comment: C: how to get low depth variants in vcf file (hetrozygous condition)
... Here's the image. This position didn't show up in vcf file https://photos.google.com/photo/AF1QipMLEdRITV4Fq82Vg0_nK_cILfbZLqfSh20czReS ...
written 7 days ago by hafiz.talhamalik230 • updated 7 days ago by Pierre Lindenbaum125k
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Comment: C: how to get low depth variants in vcf file (hetrozygous condition)
... I used SAMTOOLS for variant calling and for filteration I used mapping quality greater then 20 ...
written 7 days ago by hafiz.talhamalik230
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how to get low depth variants in vcf file (hetrozygous condition)
... I want to get a variant in vcf file which is present in hetrozygous condition. for example if at a specific position 50 reads get mapped and 26 of them are same as reference and 24 reads have an alternate allele. that specific position didn't show up as variant in vcf file. But I want them in vcf fi ...
next-gen alignment snp written 7 days ago by hafiz.talhamalik230
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Getting information of individual sample from merged sample
... I have a merged vcf file, last 8 columns are about the information of my 8 sample weather variant was there in the respective sample or not ? 3 196139511 . C A 122 PASS VDB=0.101032;RPB=-1.22822;AF1=0.5;AC1=1;MQ=60;FQ=125;PV4=1,1,1,1;DP=13;DP4=3,4,3,3;AN=2;AC=1 GT:PL:GQ ./.:.:. ./.:.:. ./.:.:. ...
vcf alignment sequencing written 4 weeks ago by hafiz.talhamalik230 • updated 4 weeks ago by Biostar ♦♦ 20
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Answer: A: HTSeq-count, Differential Gene Expression using a GFF to count exons annotations
... can you post command you are using ? tool have option for gene based count ...
written 8 weeks ago by hafiz.talhamalik230
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Comment: C: tools for MLST analysis
... yes I did. the ones I found out were paid ...
written 9 weeks ago by hafiz.talhamalik230
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tools for MLST analysis
... is there any tool to perform MLST analysis of bacterial whole genome samples/assembly ?? ...
wgs ngs next-gen written 9 weeks ago by hafiz.talhamalik230
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Answer: A: Assembly quality check
... Use [quast][1] [1]: https://github.com/ablab/quast tool. it will give you required stats. ...
written 9 weeks ago by hafiz.talhamalik230
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Comment: C: Extract Transcript sequence from fastq file (Plant RNA-Seq data)
... yes it's known one Brassica Napus. I tried reference based assembly using trinity but assembly results were not good..!! any other good assembler ?? ...
written 10 weeks ago by hafiz.talhamalik230

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