User: prasundutta87

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Posts by prasundutta87

<prev • 16 results • page 1 of 2 • next >
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mpileup BAQ score
... Hi, I was calling variants from RNAseq data using samtools mpileup|bcftools call. I am aware that the BAQ (base alignment quality) strategy is invoked by default in mpileup. BAQ is in itself derived from the original base quality score. Now if the BAQ is lower, no variants will be called in that ba ...
alignment snp rna-seq sequencing written 1 hour ago by prasundutta870
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variant calling using reference transcriptome
... Hi, Is there any tool which uses a reference transcriptome to call variants instead of a reference genome ? I will also like to use the reference transcriptome for variant annotation as well and would like to know if any variant annotation tools allows that. I did not find any tool optimised to wor ...
reference transcriptome rna-seq snp written 17 days ago by prasundutta870
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Comment: C: variant annotation issue
... Yes..the genome/transcriptome is not complete..what I will do is that I will complement my rnaseq variant calling with DNAseq data variant call and hopefully get a consensus.. ...
written 18 days ago by prasundutta870
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SnpEff using -onlyprotein option (meaning-Only use protein coding transcripts)
... Hi, My aim was to get variation information/annotation about some of my genes of interest whose differential expression details I got from their RNAseq data. Since, my variant calling tool will give information of all non-coding genes and probable unknown genes as well, I decided to annotate the ...
gene software error rna-seq snp written 19 days ago by prasundutta870
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Comment: C: variant annotation issue
... Yes..I am trying to do that with VEP..but ensemble does not have water buffalo genome. I am trying to use their standalone Perl version and custom use it by using the water buffalo genome and annotation file present in NCBI Genome database. ...
written 19 days ago by prasundutta870
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Comment: C: variant annotation issue
... The thing is that I annotated the variants using SNpEff using -onlyprotein option (meaning-Only use protein coding transcripts). I though that becasue of this non-coding genes and probable genes will be avoided becasue I am focusing on only specific type of genes. I guess -onlyprotein option did not ...
written 20 days ago by prasundutta870
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Comment: C: variant annotation issue
... I hope I am not missing anything logically. I am not sure what exactly to look for or check in order to find the reason behind it. Any suggestion is welcome. ...
written 20 days ago by prasundutta870
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Comment: C: variant annotation issue
... Yes. I did. There us only one draft assembly present in the NCBI genome database for a Mediterranean water buffalo. ...
written 20 days ago by prasundutta870
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variant annotation issue
... Hi, I have recently performed a variant annotation using Snpeff in water buffalo. The variants were called through bcftools call program (multiallelic caller) from Samtools package and are based on RNAseq reads. The BAM files were produced by aligning the RNAseq reads on the water buffalo genome av ...
software error genome alignment rna-seq snp written 20 days ago by prasundutta870 • updated 20 days ago by Brian Bushnell10k
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detecting allele specific expression of a gene at a specific locus without having any information about parental genomes
... Hi, I have RNAseq data of a water buffalo based on which I have got SNV and INDEL information in a VCF file (all variants annotated as well). Is it possible to decipher allele specific expression information from such data? Unfortunately, I do not have their parental genome information. Any logica ...
gene alignment rna-seq snp written 23 days ago by prasundutta870

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