User: prasundutta87

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Posts by prasundutta87

<prev • 26 results • page 1 of 3 • next >
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Comment: C: HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
... Thanks Devon..that seems to be the only way now.. ...
written 13 days ago by prasundutta870
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Comment: C: HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
... I am not completely sure. As a trend, the reads with highest mapping quality always has NH:i:1 (mostly applicable to newly developed aligners which report the NH tag). The issue is that some reads which have the score as 255, have NH:i:2 or NH:i:3 as well. Also, some reads which have NH:i:1 have sco ...
written 16 days ago by prasundutta870
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Comment: C: HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
... Thanks for your reply. But that was the reason the Hisat developers changed it from 255 to 60 from v2.0.4 onwards. ...
written 16 days ago by prasundutta870
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HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
... Hello, For an allele specific expression analysis, one of the ways to reduce ambiguous mapping reads is to extract or use only unique mapping (not referring to primary alignment or unique alignment here) reads from an alignment file. For this, highest MAPQ score (column 5 in a BAM file) can be use ...
alignment allele specific expression written 16 days ago by prasundutta870
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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 7 weeks 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 7 weeks 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 7 weeks 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 7 weeks 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 7 weeks ago by prasundutta870 • updated 7 weeks ago by Devon Ryan65k
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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 8 weeks ago by prasundutta870

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