User: divya

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divya20
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2 months, 3 weeks ago
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1 year, 6 months ago
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Posts by divya

<prev • 20 results • page 1 of 2 • next >
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Comment: C: How to deal with MSTRG tag without relevant gene name?
... Hello everyone, I also have above same problem i.e; ( in my case Cuffdiff gives gene ID but there specific gene names are missing) I used reference.gtf file during every steps. I also try to get specific gene name using there chr. locus number but no result found, did blast also. No any information ...
written 3 months ago by divya20
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Popoolationte Samro.pl error
... Hello everyone, I am using Popoolationte tool. While using tool an error message occur i.e; " sam is not empty in the end at samro.pl line 114, <$fh> line 113468176." while using Samro.pl script for paired-end of Popoolationte. Both the given input sam files are equal in size. I am not get ...
popoolationte samformat written 11 months ago by divya20
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Comment: C: Samtools mpileup degenerative characters
... Thanks for the comment @ Saumel That I know the -1 are the indels but I didn't get why these "y" and "s" characters also encounter with -1 in the mpileup file. ...
written 12 months ago by divya20
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Comment: C: Samtools mpileup degenerative characters
... Hello sir, Now I installed samtools version-1.5 but the problem is persist in the mpileup file. Any suggestion. ...
written 12 months ago by divya20
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Comment: A: Samtools mpileup degenerative characters
... Thanks for your reply, I m using samtools version `0.1.19-96b5f2294a` Here below I m posting the command samtools mpileup -f ref_genome.fa input.bam > output.mpileup Error lines 2 3616324 A 211 .,,.,..,-1y...,..,,..............,,,,,,......,,,...,,,....,,,....,,,,,,,.....,,..,....... ...
written 12 months ago by divya20 • updated 12 months ago by Istvan Albert ♦♦ 77k
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Samtools mpileup degenerative characters
... Hello everyone, I am using samtools to get mpileup file. but there is an degenerative characters "-1y, -1Y, -1s" etc. also shown in the mpileup file. I want to know why these degenerative characters are shown in mpileup file. Please help me to sort the above problem. Thanks, Divya ...
samtools degenrative characters mpileup written 12 months ago by divya20 • updated 3 days ago by swbarnes23.8k
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Comment: C: Popoolation variance-sliding.pl output shows only zero value
... Please anyone guide me how to solve this error. ...
written 12 months ago by divya20
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Popoolation variance-sliding.pl output shows only zero value
... Hello I am using Popoolation tool to calculate Tajima's D, Pi, and Watterson's Theta of my pool population by using "Variance-sliding.pl" script from mpileup data file . But the output generated shows 0 value in 3rd and 4th column and in 5th show "na". Eg: 4 125000 0 0.000 na 4 1 ...
popoolation tajima's pi samtools pileup tajima's d written 12 months ago by divya20 • updated 5 months ago by antaky0
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STRUCTURE software file format
... Hello, I am optimizing STRUCTURE software for the population genetics analysis. I have a gatk-vcf output file, and tried to convert with plink tool to STRUCTURE file format, but the output is not appropriate, so how to convert vcf file to structure file format. when I load data in STRUCTURE error ...
populationgenetics structure snp written 13 months ago by divya20
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extract SNP, variants
... Hello everyone, Is there any tool or command to find out SNP, indels, genome coverage, X-coverage from .bam file. Thanks, Divya ...
indel variant calling snp rna-seq mapping written 15 months ago by divya20 • updated 15 months ago by AB90

Latest awards to divya

Popular Question 12 weeks ago, created a question with more than 1,000 views. For extract SNP, variants
Popular Question 9 months ago, created a question with more than 1,000 views. For R unused arguments

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