User: prasundutta87

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prasundutta87150
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Posts by prasundutta87

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Comment: C: excessive loading time for VCF files in IGV
... Yes...everything loads fine.. ...
written 25 days ago by prasundutta87150
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Comment: C: excessive loading time for VCF files in IGV
... It loads..but after very long time leading to time wastage..the genome used is correct only.. ...
written 25 days ago by prasundutta87150
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Comment: C: excessive loading time for VCF files in IGV
... There is only one sample..and very small number of variants (only 25) as its only for one gene..The VCF file is bgzip+tabix indexed.. ...
written 25 days ago by prasundutta87150
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excessive loading time for VCF files in IGV
... Hi, Has anyone faced an issue in which an indexed VCF file takes ages to load in IGV? If they have, is there a workaround? I am running IGV v2.3.72 in Java 1.8 in Windows. I have tried latest version of IGV as well, it has the same issue. ...
visualization snp igv written 25 days ago by prasundutta87150
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Comment: C: some good practices doubts
... Ok..thanks for letting me know this. The coordinate screw ups do make sense..and bcftools mpileup also has the option to provide specific coordinates to perform selective variant calling.. ...
written 26 days ago by prasundutta87150
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some good practices doubts
... Hi, I have a paired end DNA sequence alignment BAM file (got from using BWA -M) and would like to know if the points mentioned below is a good practice.. 1) Since my aim is to perform variant calling, is it OK to keep unmapped, secondary,singleton and duplicated marked reads in the BAM file itself ...
gene variant calling alignment written 26 days ago by prasundutta87150 • updated 26 days ago by WouterDeCoster24k
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Answer: A: How to extract reads with a known variant form a bam file
... The mpileup function is the best tool for this kind of job..try using the latest version though (1.6) as they have a new switch (qname) that allows you to get the read names of the piled up reads as well..the usage is pretty simple, many examples are present on the web..you can Google it out.. other ...
written 26 days ago by prasundutta87150
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Answer: A: annotating strand orientation
... There is nothing called as strand orientation during variant calling. By default, variants are reported in the forward strand only. That also means that there is a variation in the reverse strand in the same position as well. Variant callers don't have any information about transcript orientation as ...
written 27 days ago by prasundutta87150
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Answer: A: extract only geneID and gene symbol from GTF file
... best tool for this..http://gffutils.readthedocs.io/en/latest/GTF_extract.html ...
written 5 weeks ago by prasundutta87150
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strand information issue for overlapping exons
... Hi, I am using hisat2 (v2.4.0) for aligning my stranded RNAseq data and just stumbled upon a downstream analysis issue of which reads come from forward and which reads come from reverse strand. This is because I got an variation in a position present in overlapping exons. One exon is present in the ...
alignment rna-seq exon written 5 weeks ago by prasundutta87150

Latest awards to prasundutta87

Scholar 4 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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