User: hafiz.talhamalik
hafiz.talhamalik • 240
- Reputation:
- 240
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- Location:
- Pakistan
- Twitter:
- @hafizmuhdtalha
- Last seen:
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- Joined:
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Posts by hafiz.talhamalik
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... Thanx. let me try that.. ...
written 21 days ago by
hafiz.talhamalik • 240
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... How can I extract ribosomal DNA data from whole genome dna sequencing data ? any specific tool available for this purpose ? or if someone guide me how to do it ? ...
written 21 days ago by
hafiz.talhamalik • 240
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... ok..!! May be I m wrong but Tassel is mainly designed for maize which is diploid. ...
written 6 weeks ago by
hafiz.talhamalik • 240
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5 follow
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... I have a GBS data for wheat. I mapped it to reference and then used freebayes for variant calling. it has the option for ploidy. so should I used 6 or 2 ? bcoz as wheat is hexploid but the reference has chromosomes sequences as 1A, 1B and 1C. so keeping in mind I should be using the parameter ploid ...
written 6 weeks ago by
hafiz.talhamalik • 240
• updated
6 weeks ago by
JC ♦ 11k
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Answer:
A: Snpcalling with replicates
... You should map individual sample and then make a combined vcf file.
Its always good to make merged vcf file using from bam files rather than making individual vcf files and then merging it. ...
written 7 weeks ago by
hafiz.talhamalik • 240
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... I am using BPGA linux based tool for pan genome analysis. It runs quite fine and give me results. the only issue is coloring of plots. all plots made by the pipeline are of black/grey color.
How can I made them interactive ? is there is any issue in library ?
someone kindly guide me.
...
written 7 weeks ago by
hafiz.talhamalik • 240
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... I want to perform COG analysis on my whole genome data. NCBI's database is there but I m not getting an idea how to use that. Is there any tool to perform this analysis?or if someone could help me how to use NCBI's COG database ? ...
written 8 weeks ago by
hafiz.talhamalik • 240
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Comment:
C: no single output file from maker
... yup that's the case with me.. I thought I will get a single output file. ...
written 8 weeks ago by
hafiz.talhamalik • 240
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137
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Comment:
C: no single output file from maker
... It's completely finished.
Log files shows some error in some contigs rest looks fine.
...
written 9 weeks ago by
hafiz.talhamalik • 240
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... I ran MAKER tool for plant genome annotation. It last almost 2 weeks and there is no single final file as an output/result. there are hundred's of individual protein files but not a single gff file. why is it so ?? ...
written 9 weeks ago by
hafiz.talhamalik • 240
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