User: prasundutta87

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prasundutta87130
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Posts by prasundutta87

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Comment: C: variant calling by GATK question about alignment
... Why are you spamming here?? It has nothing to do with this post.. ...
written 1 day ago by prasundutta87130
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Comment: C: detecting allele specific expression of a gene at a specific locus without havin
... I have performed the one sample analysis and have followed their protocol from their manual..I have been having discussions with the author (Oleg) and have shared my methodology with him and all seems to be on track.. ...
written 4 weeks ago by prasundutta87130
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Comment: C: long reads Pacbio SNP calling
... GATK is not suitable for calling variants using long reads..they are developed, tested and verified keeping short reads (such as illumina) in mind..this particular github tool (by pacific biosciences itself) can be checked for variant calling - https://github.com/PacificBiosciences/GenomicConsensus ...
written 5 weeks ago by prasundutta87130
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Comment: C: allelic unbalance for multiplex PCR based amplicon data
... Finding a solution to such a problem during genotype assignment and variant calling is not very easy as it depends on a variety of factors such as sequence and mapping errors that any variant calling software takes into consideration. Some of them can be taken care using methods mentioned by Kevin. ...
written 5 weeks ago by prasundutta87130
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Comment: C: detecting allele specific expression of a gene at a specific locus without havin
... Hi..thanks for your answer..I have come across this tool after I used and got results using MBASED, another tool that gives gene based ASE without requiring parental genomes or phasing information.. ...
written 5 weeks ago by prasundutta87130
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Comment: C: Homozygous exonic markers from AI analysis
... I guess before attempting this kind of analysis, you should go through this video where it is very nicely and clearly explained the 'what' and 'why' aspects of allele specific expression (ASE)- http://medias01-web.embl.de/Mediasite/Play/7a15ffa352f64224a9cdd990c8bc64e01d Furthermore, as Fabio menti ...
written 5 weeks ago by prasundutta87130
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Answer: C: How to find nu. of variants present in a gene for my Exome seq. sample
... You can annotate your variants using variant annotation tools such as SnpEff/Annovar/VEP and you can filter your vcf file using your gene of interest to get only those variants that has an effect on your gene of interest.. The second way is what I guess genomax is pointing you towards (correct me i ...
written 5 weeks ago by prasundutta87130
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Comment: C: How to find out the insert size in RNA seq data
... As Chris suggested, you need to align your reads to get a SAM/BAM file and then run 'samtools stats' to get information about insert sizes..it will also give you an insert size distribution graph.. ...
written 6 weeks ago by prasundutta87130
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Comment: C: Alignment of two different file format
... This question can be answered by just runnning your python program and seeing if you get any errors..I haven't tried it but you may definetly get errors because .fna just contains the nucleic acid sequence whereas fastq contains your sequence with their corresponding quality scores.. To convert fas ...
written 6 weeks ago by prasundutta87130
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Answer: A: Mismatch and Indel rate in alignment
... check this out https://www.biostars.org/p/252330/ ...
written 7 weeks ago by prasundutta87130

Latest awards to prasundutta87

Scholar 9 weeks ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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