User: prasundutta87

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Posts by prasundutta87

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detecting allele specific expression of a gene at a specific locus without having any information about parental genomes
... Hi, I have RNAseq data of a water buffalo based on which I have got SNV and INDEL information in a VCF file (all variants annotated as well). Is it possible to decipher allele specific expression information from such data? Unfortunately, I do not have their parental genome information. Any logica ...
gene alignment rna-seq snp written 2 hours ago by prasundutta870
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Comment: C: SnpSift command query
... Actually since | is the OR operator, if any one condition is TRUE, then only filtering will take place. When && or AND operator is used, it means that if all the conditions are TRUE together, only then filtering will take place. Since, one variant willl have only one effect in the first a ...
written 8 days ago by prasundutta870
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Comment: C: SnpSift command query
... Thank you for the suggestion. I used it just now. No filtering was performed on my input file..furthermore the operator '&&' doing the job does not make sense. Is there a catch somewhere that I am missing? ...
written 9 days ago by prasundutta870
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SnpSift command query
... Hi, I wish to exclude all the variants in a vcf file where the first snpeff annotation is either intron_variant or 'splice_acceptor_variant&intron_variant or 'splice_region_variant&intron_variant' or 'splice_donor_variant&intron_variant. Now the command that does NOT work is: java ...
software error snp written 10 days ago by prasundutta870 • updated 9 days ago by Robert Sicko460
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Comment: C: difference in genotypes in a multisample vcf file
... Thanks a lot..am trying out GATK as well although the tools take too much time to run. ...
written 11 days ago by prasundutta870
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Answer: A: difference in genotypes in a multisample vcf file
... Thanks for your reply Petr. Just to add, I did call the SNPs using both individual's data (alignment file) simultaneously. Also, both of my alignment files are sorted and indexed before I used them for calling variants. The resulted VCF file is a multi-sample VCF file. Hence, I have genotype data si ...
written 12 days ago by prasundutta870
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difference in genotypes in a multisample vcf file
... Hi, I have two individuals of the same animal (one male and one female water buffalo). I have RNAseq data from both the animals and I used mpileup and bcftools 'call' programs for variant calling. My aim is to find out allelic imbalance in a set of genes of interest. Let me take an example of one ...
next-gen snp rna-seq written 12 days ago by prasundutta870

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