User: prasundutta87

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Posts by prasundutta87

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Comment: C: RNA Seq data network analysis
... Check out Miru: https://kajeka.com/miru/miru-about/ It can be extensively used for RNAseq network analysis for deciphering co-expression of genes involved.. ...
written 1 day ago by prasundutta870
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Comment: C: strand bias filter for strand specific RNAseq data variants
... I was giving it a thought and was just going to write it..you replied before..hehe..but yes.. according to my understanding, there won't be any reads arising from the opposite strand ( based on which strand is chosen for sequencing based on needs)..thanks anyway.. correct me if I am wrong.. ...
written 3 days ago by prasundutta870
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Comment: C: strand bias filter for strand specific RNAseq data variants
... Hi, Could you kindly let me know why it should not be used in single end strand specific library? ...
written 4 days ago by prasundutta870
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Comment: C: strand bias filter for strand specific RNAseq data variants
... Thanks..is it same is this? https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_annotator_FisherStrand.php I was wondering if SP and FS (from GATK) are calculated in the same manner. ...
written 4 days ago by prasundutta870
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Comment: C: strand bias filter for strand specific RNAseq data variants
... Thanks for your quick reply. I am using paired-end reads. Currently in some on my analyses I have included variants where SP <= 60 (based on some literatures). Unfortunately, I am unable to understand how SP in samtools is calculated and would like to know that as well just to be sure if I have c ...
written 4 days ago by prasundutta870
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strand bias filter for strand specific RNAseq data variants
... Hi, Can someone let me know if there is a need of filtering variants based on strand bias (SP tag of samtools) for a strand specific RNAseq data? I am trying to understand its concept specifically for strand specific RNAseq data for which I haven't got any document. ...
rna-seq snp written 4 days ago by prasundutta870 • updated 4 days ago by Devon Ryan68k
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priors for calculting genotype likelihood using RNAseq data
... Can anyone point me to a literature or explain the need of population priors during genotype likelihood estimation using RNAseq data? I did get results connected to DNAseq. I am using bcftools mpileup (v1.4) for likelihood estimation and then genotype calling and variant calling using bcftools call ...
rna-seq written 19 days ago by prasundutta870
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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 6 weeks 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 7 weeks 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 7 weeks ago by prasundutta870

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