User: prasundutta87

gravatar for prasundutta87
prasundutta87160
Reputation:
160
Status:
Trusted
Location:
Last seen:
22 hours ago
Joined:
1 year ago
Email:
p************@gmail.com

Posts by prasundutta87

<prev • 92 results • page 1 of 10 • next >
0
votes
2
answers
136
views
2
answers
Comment: C: addressing software versions
... Luckily I ran with default parameters and had not set -mbq..and I am running the gvcf generation per sample now..theoretically it should not change at all..but again..as genomax suggested..from a publication point of view, this change of version will be a difficult thing to sell..the reviewers will ...
written 12 days ago by prasundutta87160
0
votes
2
answers
136
views
2
answers
Comment: C: addressing software versions
... I agree with that..from a publication point of view, it definitely makes sense..I am just concerned over the time being wasted.. ...
written 12 days ago by prasundutta87160
0
votes
2
answers
136
views
2
answers
addressing software versions
... Hi, I started using GATK v4.0.0.0 on some of my WGS samples some days back. Few samples got a bug- "HaplotypeCaller exception: contig must be non-null and not equal to *, and start must be >= 1". I checked online and found that this bug was solved in the new sub-version. I downloaded GATK v4.0 ...
software error gatk best practices written 12 days ago by prasundutta87160
1
vote
1
answer
195
views
1
answers
Comment: C: fastqc adapter content
... Sequencing can never be perfect, at least looking into the current scenario of the advent of long reads...it's also difficult to draw lines between what is right and what is an artifact or error..these are evolving technologies..and marketing plays a key role in making things even more difficult.. ...
written 17 days ago by prasundutta87160
0
votes
1
answer
195
views
1
answers
Comment: C: fastqc adapter content
... Thanks a lot for your views..I will do that.. ...
written 17 days ago by prasundutta87160
0
votes
1
answer
195
views
1
answers
Comment: C: fastqc adapter content
... Thanks..I can understand the points..On just grepping my data with Truseq adapter data found in https://support.illumina.com/bulletins/2016/12/what-sequences-do-i-use-for-adapter-trimming.html , I also found adapters in the middle of the reads..can it they be just artifacts? Because, from my multiqc ...
written 17 days ago by prasundutta87160
0
votes
1
answer
195
views
1
answers
Comment: C: fastqc adapter content
... Thanks genomax. I scanned the reads and got adapters. My sequencing facility did not remove adapters.Since my main goal is calling variants from the reads, the adapter bases will anyway have lower base qualities and while mapping to the genome also may be soft clipped (using BWA mem here). Furthermo ...
written 17 days ago by prasundutta87160
8
votes
1
answer
195
views
5 follow
1
answer
fastqc adapter content
... Hi, I made a multiqc plot collating many fastqc files from paired end WGS reads. I got a warning in adapter content step, but there was nothing present in overrepresented sequences bit. What could be the issue? How do I interpret this? The read length is 250 and no trimming has been done. I am una ...
sequencing quality control fastqc written 17 days ago by prasundutta87160 • updated 17 days ago by GenoMax42k
0
votes
0
answers
115
views
0
answers
Comment: C: heterozygosity during variant calling in a non-model organism such as Bubalus Bu
... Hi Dylan..there is only one reference genome..and I am using that for variant calling..there is a recent paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185220 In table 1, there is some data on heterozygosity, is it what I should look into? If yes, How should I interpret it ...
written 29 days ago by prasundutta87160
0
votes
0
answers
115
views
0
answers
heterozygosity during variant calling in a non-model organism such as Bubalus Bubalis
... Hi, I am not from a population genetics background, but am doing a feasibility test using a few organisms for a bigger aim of determining allele specific expression (ASE). I am performing variant calling on DNA-seq samples from 4 water buffaloes (*Bubalus bubalis*) to determine heterozygous sites i ...
next-gen dna-seq snp sequencing written 29 days ago by prasundutta87160

Latest awards to prasundutta87

Scholar 6 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 571 users visited in the last hour