User: hafiz.talhamalik
hafiz.talhamalik • 230
- Reputation:
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- Pakistan
- Twitter:
- @hafizmuhdtalha
- Last seen:
- 3 days ago
- Joined:
- 4 years, 2 months ago
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Posts by hafiz.talhamalik
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... what's in ur expt variable ?? how many replicates ?? ...
written 7 days ago by
hafiz.talhamalik • 230
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... 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.talhamalik • 230
• updated
7 days ago by
Pierre Lindenbaum ♦ 125k
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... I used SAMTOOLS for variant calling and for filteration I used mapping quality greater then 20 ...
written 7 days ago by
hafiz.talhamalik • 230
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... 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 ...
written 7 days ago by
hafiz.talhamalik • 230
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... 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 ./.:.:. ./.:.:. ./.:.:. ...
written 4 weeks ago by
hafiz.talhamalik • 230
• updated
4 weeks ago by
Biostar ♦♦ 20
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102
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... can you post command you are using ? tool have option for gene based count ...
written 8 weeks ago by
hafiz.talhamalik • 230
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150
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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.talhamalik • 230
7
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150
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... is there any tool to perform MLST analysis of bacterial whole genome samples/assembly ?? ...
written 9 weeks ago by
hafiz.talhamalik • 230
2
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1
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179
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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.talhamalik • 230
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... 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.talhamalik • 230
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