User: shreyasibiswas88

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Posts by shreyasibiswas88

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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 1 day 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 1 day ago by shreyasibiswas8830 • updated 1 day ago by Ram15k
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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 3 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 3 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 5 months ago by shreyasibiswas8830 • updated 5 months ago by WouterDeCoster29k
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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 8 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 10 months ago by shreyasibiswas8830 • updated 14 days ago by lxw340
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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 11 months ago by shreyasibiswas8830
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Determining the correct reading frames for transcripts for dn/ds calculation
... Hi everyone, I am trying to calculate genome-wide dn/ds ratio between two closely related rat species using PAML. I have genome co-ordinates for transcript orthologs for the two species. However, I am not able to figure out how to decide the reading frame for translating the sequences in to amino a ...
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Comment: C: Matching fasta headers in a file and removing the entries that do not have a cor
... UPDATE: I think I figured out what the problem is. The unique entries are not based on rn5_x_xx but NMxx_rn5_x_xx. So I have more than one sequence for each entry in my.list. That was a total carelessness on my part to not have noticed that. Trying to now modify the cut command to make my.list with ...
written 17 months ago by shreyasibiswas8830

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Popular Question 16 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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