User: shreyasibiswas88

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Posts by shreyasibiswas88

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Comment: C: Samtools mpileup returns empty vcf file
... I have checked and re-checked without any success. It is bizarre to me as it has worked in the past. I have written to the authors too. But haven't heard anything back. Thank you for your suggestions. ...
written 5 months ago by shreyasibiswas8830
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2/50 inidividuals show missing data at almost all positions in final vcf generated using HaplotypeCaller
... Hello all, I used HaplotypeCaller from GATK to generate VCF from 50 individuals. My reference is Rattus norvegicus and 48/50 individuals are Rattus norvegicus. The remaining two individuals are Rattus rattus species. The WGS for these two individuals have been mapped on the same reference, Rattus n ...
vcf gatk haplotypecaller missingdata written 5 months ago by shreyasibiswas8830
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Comment: C: Samtools mpileup returns empty vcf file
... Thank you for your response. I followed your suggestion. Unfortunately it still doesn't work. i have successfully used the above command in the past without the `-` as suggested by you in generating vcf from 10 bam files. ...
written 5 months ago by shreyasibiswas8830
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Samtools mpileup returns empty vcf file
... Hello everyone, I am using samtools mpileup on multi bam files to genrate vcf file. mpileup seems to be working with only 6 bam files but not on more than 6 files. If I enter more than 6 files, samtools finishes without error in approx 2min and the vcf file generated is empty except for the header ...
samtools mpileup written 5 months ago by shreyasibiswas8830 • updated 5 months ago by RamRS19k
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bioperl fasta indexing problem with non model genome sequence
... Hello all, I am new to using bioperl and trying to extract the mRNA transcript for every gene from a reference fasta and gff file. I have used the Bioperl script provided in a similar query https://www.biostars.org/p/46281/ (by user @severin) and this script works great for reference genome of mou ...
mrna fasta bioperl reference index written 9 months ago by shreyasibiswas8830
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Comment: C: Extract Cds Fastas From A Gff Annotation + Reference Sequence
... Hi Federico, I am new to this and trying to extract the longest CDS in the right reading frame using gff3 file. This script works great to extract CDS. However, I am not able to tell if it is extracting the longest transcript or any one transcript for every gene. I see *s in the corresponding peptid ...
written 9 months ago by shreyasibiswas8830
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Make fasta sequence of specific lengths from Vcf file of specific lengths
... Hi all, I have a multi-sample vcf file of 350 loci spread across the genome from 85 individuals. I want to use this to ultimately build phylogenetic trees. For this i want to first make fasta sequences of 100kb length for each of the 350 loci for the 85 individuals, something similar to what GATK F ...
vcf gatk phylogenetic tree fastareference snp written 10 months ago by shreyasibiswas8830 • updated 10 months ago by WouterDeCoster35k
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Should I average dN/dS over all CDS for a gene or consider only the longest transcript?
... Hi everyone, I have calculated dN/dS ratio for ALL transcripts for ALL genes for my study systems (different species of rats) using codeml in PAML. Now I am not able to decide on what is the dN/dS for the entire gene (i.e all the CDS for a gene). Should I take an average of dN/dS ratio for all CDS ...
longest transcript average dn/ds dnds paml written 14 months ago by shreyasibiswas8830
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yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
... Hi everyone, I am running yn00 to analyze around 35000 alignments. My codon alignments were generated by pal2nal in PAML input format. When I run the yn00, dn,ds is calculated only for around 300 alignments but not for the rest ~34000 alignments. I tried running these alignments one by one and I g ...
pal2nal phylip paml input file written 16 months ago by shreyasibiswas8830 • updated 2 days ago by al-ash60
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Comment: C: Determining the correct reading frames for transcripts for dn/ds calculation
... I have the nucleotide sequences of all transcripts. I can't decide which reading frame to translate each one into. Should I select the longest ORF for each transcript? ...
written 16 months ago by shreyasibiswas8830

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Popular Question 22 months ago, created a question with more than 1,000 views. For Error while trying to get consensus Fastq from BAM

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