User: nabiyogesh

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nabiyogesh50
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50
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Location:
South Korea
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7 minutes ago
Joined:
4 months, 4 weeks ago
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n*********@gmail.com

Posts by nabiyogesh

<prev • 161 results • page 1 of 17 • next >
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Query related to SNP calling from RNAseq data using GATK
... I have few queries related to SNP detection in RNAseq data: 1) Is it required to do Indel Realignment and Base Recalibration while calling SNP from RNAseq data? 2) When I used RNAseq data for SNP calling, I also got SNP in intron region.why? ...
snp written 2 minutes ago by nabiyogesh50
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Comment: C: GATK on RNASeq/ChIP data - distinction between no SNP and no data.
... Hi John, I am also interested in identifying SNP in RNAseq data. I am also using GATK pipeline. do you think Indel Realignment and Base Recalibration needed while calling SNP from RNAseq data? ...
written 36 minutes ago by nabiyogesh50
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Answer: A: SNP analysis based on RNAseq data using GATK PIPELINE
... Thanks a lot. please also suggest Do I need to do Indel Realignment and Base Recalibration while calling SNP from RNAseq data? If yes, then How do I get these two files for Indel Realignment: -known indels.vcf \ -targetIntervals intervalListFromRTC.interval ...
written 10 hours ago by nabiyogesh50
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Answer: A: SNP analysis based on RNAseq data using GATK PIPELINE
... Thanks a lot. Can you please also suggest which quality score can be used as a cutoff to find confirm SNP. What are the other parameter to filter raw VCF? ...
written 11 hours ago by nabiyogesh50
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SNP analysis based on RNAseq data using GATK PIPELINE
... Hi... I have analyzed SNP in two contrasting genotypes based on RNAseq data using GATK pipeline. In some cases, there is a string of nucleotide in the reference position and the only single alternate nucleotide in genotype. what does it mean? After calling SNP by using GATK, How should I filter r ...
snp written 11 hours ago by nabiyogesh50
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Comment: C: Error building database in snpEff
... Thanks. It is resolved. ...
written 1 day ago by nabiyogesh50
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Comment: C: Error building database in snpEff
... Sorry, I am not able to understand in which folder I should store gtf and fasta file.... and which path and name should I mention in snp.Eff.config. My fasta file name is Radish.fasta gtf file name is genes.gtf ...
written 1 day ago by nabiyogesh50
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Error building database in snpEff
... I am getting some error while building database in SnpEff: java -jar /home/yog/software/snpEff/snpEff.jar build -gtf22 -v genome 00:00:00 SnpEff version SnpEff 4.3k (build 2017-03-29 17:16), by Pablo Cingolani 00:00:00 Command: 'build' 00:00:00 Building database for 'ge ...
rna-seq written 1 day ago by nabiyogesh50 • updated 1 day ago by Santosh Anand1.5k
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Comment: C: STAR-2 PASS raw read mapping for SNP calling using GATK
... Thank a lot WouterDeCoster! I will try it once the mapping is complete for all file. ...
written 3 days ago by nabiyogesh50
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Comment: C: STAR-2 PASS raw read mapping for SNP calling using GATK
... Hi, My SJ.out.tab file name for multiple sample is like this: 216_5W_CaSJ.out.tab 216_7W_CaSJ.out.tab 218_5W_CaSJ.out.tab 216_7W_CaSJ.out.tab 216_7W_CoSJ.out.tab 216_7W_CoSJ.out.tab will it work if I use --sjdbFileChrStartEnd *.out.tab ...
written 3 days ago by nabiyogesh50

Latest awards to nabiyogesh

Centurion 5 weeks ago, created 100 posts.
Supporter 3 months ago, voted at least 25 times.
Rising Star 3 months ago, created 50 posts within first three months of joining.

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