User: prasundutta87

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prasundutta87250
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Posts by prasundutta87

<prev • 131 results • page 1 of 14 • next >
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Comment: C: allele specific expression (ASE) reference ratio plot query
... Hi Vitis, Thanks for the reply. I have not done that. My basic QC was limited to fastqc visualisation and trimming. I forgot to mention that the problematic samples are from total RNA-seq. My 14 samples have a mix of mRNA-seq and total RNA-seq samples. I have updated my post now. ...
written 1 day ago by prasundutta87250
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allele specific expression (ASE) reference ratio plot query
... Hi, To check for ASE, I performed multisample gDNA variant calling using GATK and got heterozygous biallelic sites for which I looked for RNA-seq read counts for both Ref and Alt alleles at those sites. I used allelecounter (v0.6) for that (https://github.com/secastel/allelecounter). More informati ...
allele-specific expression rna-seq snp written 2 days ago by prasundutta87250
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runtime error in LDhat
... Hi, I got a runtime error while running LDhat 'pairwise' program. I need some help to understand the issue so that I can take care of it. The command was: pairwise -seq chr1.ldhat.sites -loc chr1.ldhat.locs -lk ../new_lk.txt The error: > Run-time error > > allocation failure 2 in i ...
genome ldhat snp population genetics written 2 days ago by prasundutta87250
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Comment: C: Filtering results difference amongst VCF files
... Just checked that after running 'samtools depth' with -a option on only chromosome 1 for all 4 samples. There are more low depth regions for the sample with less remaining variants. There were 39118 more loci with 0 depth than the sample having the second highest number of loci with 0 depth. It was ...
written 11 days ago by prasundutta87250
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Comment: C: Filtering results difference amongst VCF files
... Thanks a lot for the hint! :-) ...
written 11 days ago by prasundutta87250
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Comment: C: Filtering results difference amongst VCF files
... Ok. So, after obtaining the multisample VCF file after adapting the GATK multisample variant calling pipeline, only biallelic SNPs were obtained using this command: bcftools view -v snps -m2 -M2 --threads 8 |bgzip --threads 8 > Then I performed hard-filtering on the multisample VCF file to ...
written 12 days ago by prasundutta87250
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Answer: A: How to analysis mutations effects bioinformatically?
... Some of your questions can be answered by "variant annotation". You can start by getting an overview of different variant annotators from this link: http://blog.goldenhelix.com/goldenadmin/the-sate-of-variant-annotation-a-comparison-of-annovar-snpeff-and-vep/ Then you can google out individual pape ...
written 13 days ago by prasundutta87250
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Filtering results difference amongst VCF files
... Hi, I have performed a multisample variant calling on 81 non-human mammal samples using GATK. I wanted to do allele-specific expression analysis of 4 samples out of the 81 for which I have RNAseq data. For doing that, I selected only biallelic heterozygous variants from those 4 samples from the mul ...
gatk snp filtering variants written 15 days ago by prasundutta87250
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Comment: C: GATK 4 GenomeAnalysisTK still available? (Unable to access jarfile)
... That is right. Although, the workflow has changed in some places. The whole indel realignment step has been removed due to the reason I specified above. Also, for multisample variant calling (also called joint variant calling), the GVCF mode is used during the usage of Haplotypecaller. To know abou ...
written 23 days ago by prasundutta87250
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Answer: A: GATK 4 GenomeAnalysisTK still available? (Unable to access jarfile)
... Please use the latest version of GATK4 for any variant calling job (https://github.com/broadinstitute/gatk/releases). The variant calling workflow for Germline SNPs+Indels has also changed (https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145) The quick start guide may be help ...
written 25 days ago by prasundutta87250

Latest awards to prasundutta87

Student 1 day ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 21 days ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 4 weeks ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 10 weeks ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 3 months ago, created 100 posts.
Supporter 5 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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