User: prasundutta87

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prasundutta87360
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Posts by prasundutta87

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Comment: C: illumina sequencing dual index query
... Thanks a lot, let me go through these documents and pages. Will come back here in case of any doubts. ...
written 8 days ago by prasundutta87360
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Comment: C: illumina sequencing dual index query
... I just made them up for understanding the concept. But, to answer your question, they are from a different provider, but the sequencing has been done on an Illumina machine. But still, shouldn't the UMIs be known? Should they be asked from the protocol providers directly? ...
written 8 days ago by prasundutta87360
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Comment: C: illumina sequencing dual index query
... So, basically, the i7 index looks like this- TACTAGTANNNNNNNNN and the i5 index looks like this-GATCGACA My read header looks like this- @______:__:_________-_____:_:____:_____:____ _:_:_:TACTAGTA+GATCGACA Please let me know if this information is enough. According to me, N can be any base. Why ...
written 8 days ago by prasundutta87360
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Comment: C: illumina sequencing dual index query
... Sorry, I missed clicking 'ADD REPLY' to ATpoint's reply. Can this be changed? ...
written 8 days ago by prasundutta87360
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Comment: C: illumina sequencing dual index query
... Not really, I just have 'i7 index'+'i5 index' at the end of the read header. The i7 index is just 8 bp long. I am not understanding why do sequencing protocols have UMI as N's? Isn't it the whole point that when sequencing is done, that UMI should be known? Is there any document/website where I can ...
written 8 days ago by prasundutta87360
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illumina sequencing dual index query
... Hi, In Illumina sequencing, where dual indexes are used (i5 and i7), the i7 indexing read contains a 9bp molecular tag (UMI) in the form of 'N' in addition to the unique 8bp sample index.N can be any base. I am aware that when bcl2fastq is used for demultiplexing, both i7 and i5 index sequences are ...
sequencing written 8 days ago by prasundutta87360
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Answer: A: WES allelic imbalence
... Why are you testing for allelic imbalance using exome (DNA-seq) data? You only use DNA-seq data for genotyping sites and get high-quality heterozygous sites and then use expression (RNA-seq) data from the same organism on those sites to get allelic imbalance results. You can get a good understandi ...
written 10 days ago by prasundutta87360
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soft-clipping during alignment and variant calling query
... It is known that BWA-MEM soft-clips bases to achieve a higher alignment rate. If a variant caller is used after that, say, GATK Haplotyecaller, is it necessary to keep the parameter --dont-use-soft-clipped-bases to TRUE? Or should we keep it in default (false) as it may affect the realignment step d ...
variant calling bwa-mem alignment gatk written 4 months ago by prasundutta87360 • updated 3 months ago by Biostar ♦♦ 20
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Answer: A: allele specific expression (ASE) reference ratio plot query
... Just to update on this, the first two weird plots arose due to sample switching in the lab.. ...
written 8 months ago by prasundutta87360
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finding out SNPs from SNVs and breed specific SNPs
... Hi, I am working with a multisample VCF file for a non-model organism that contains only biallelic single nucleotide variants (SNVs). The samples belong to different breeds of the organism as well. I wish to find SNPs (single nucleotide polymorphisms), which is a population-based term (the SNV shoul ...
snv snp written 10 months ago by prasundutta87360 • updated 9 months ago by Biostar ♦♦ 20

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Popular Question 5 days ago, created a question with more than 1,000 views. For Correct way to report variant statistics from bcftools stats report
Popular Question 28 days ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 3 months ago, created a question with more than 1,000 views. For PCA implementation in plink
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Popular Question 5 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Student 6 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 6 months ago, created a question with more than 1,000 views. For HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
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Scholar 13 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
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Student 16 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 17 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
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