User: prasundutta87

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Posts by prasundutta87

<prev • 22 results • page 1 of 3 • next >
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Comment: C: deciding --max-depth for RNAseq variant calling
... I am trying to analyse allele specific expression.I have DNA sequence as well..will check for concordance/discordance between the data I will be getting from both variant calls. ...
written 21 days ago by prasundutta870
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Comment: A: deciding --max-depth for RNAseq variant calling
... Thank you for your answers. I am aware that coverage won't be consistent because genes expressing higher will have higher stack of reads aligned to them. I wanted to ask how high should I choose the threshold to capture the highly expressed genes as well without landing to any technical issue. But I ...
written 22 days ago by prasundutta870
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deciding --max-depth for RNAseq variant calling
... Hi, I have data from RNAseq experiment with a coverage of 100 million reads. Samtools mpileup has an option of --max-depth which means 'At a position, read maximally INT reads per input file'. Its default value is 250 and can be increased upto 1000000 (samtools v1.2). There is a limit/cap/default i ...
alignment sequence rna-seq written 22 days ago by prasundutta870
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Comment: C: singleton reads RNAseq downstream analysis
... Thank you for the reply. The singletoms are mapping and hence I kept them. ...
written 22 days ago by prasundutta870
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singleton reads RNAseq downstream analysis
... Hi, I am aware that for any RNAseq based downstream analysis, many uninformative reads need to be filtered, for example, low quality reads, unmapped reads, non-unique reads etc. This is based on literauture survey. How important are singleton reads (from a paired end reads RNAseq experiement) for ...
alignment rna-seq written 23 days ago by prasundutta870 • updated 22 days ago by Devon Ryan64k
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HISAT2 MAPQ scoring scheme
... Hi, On checking out MAPQ scores of my BAM file, I found that there are only three unique scores-0,1 and 60. What do the scores mean? I have checked their manual and its not mentioned there. (I am using HISAT2 version 2.0.4), where the highest score has been reduced from 255 to 60. ...
alignment written 28 days ago by prasundutta870
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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 4 weeks 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 7 weeks 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 7 weeks 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 7 weeks ago by prasundutta870

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