User: vishalchanda364

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Posts by vishalchanda364

<prev • 47 results • page 1 of 5 • next >
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Perform SNP-SNP correlation.
... Hello, I have been trying to learn more about computational biology and now I am trying to learn, GWAS where I need to correlate SNP of two different diseases for finding correlation between the diseases. While studying through the published data I learnt that for this I either require genotyped da ...
gene snp written 4 months ago by vishalchanda36420 • updated 4 months ago by colindaven2.3k
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Is building otu table in metagenomic analysis necessary?
... Hello all, I have got all my clear, putative viral/bacterial sequences from a metagenomic sequence file. Now I am not able to understand how to proceed with that. I used bowtie2 tool for aligning my sequences to reference db, and retrieved my sequences, in article which I am referring [Skoporov et ...
genome next-gen sequencing written 5 months ago by vishalchanda36420
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Cannot find out next step.?
... Hello, I was working on a metagenomic data following the pipeline explained by [Skoporov et al., 2019][1] there in a step of identifying temperate bacteriophage, they have used **hmmscan from HMMER**, I followed the steps as explained and got a table output. VOG11081 - k14 ...
sequence alignment written 5 months ago by vishalchanda36420 • updated 5 months ago by Kevin Blighe63k
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Taking out the no hit sequences.
... Hello all, I have been working around BLAST+ from last couple of days, I am running a metagenomics data, which I alinged to **Cog (Cluster of Orthologus Groups) db**, now my ultimate objective is to remove the bacterial sequences so that putative viral contigs remain back. So the hits from the BLA ...
assembly sequence alignment written 5 months ago by vishalchanda36420
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Comment: A: Generate count table using Samtools
... Thank you everyone for the help and support ...
written 5 months ago by vishalchanda36420
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Comment: C: Generate count table using Samtools
... okay Thank You so much @colindaven. I will do it now. ...
written 5 months ago by vishalchanda36420
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Comment: A: Generate count table using Samtools
... Well sorry, I couldn't frame the question properly. The article which I am referring is > The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific it can be cited [here][1], The question is that, I have similar work to the one done in this work, I too have 10 samples of metage ...
written 5 months ago by vishalchanda36420
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Generate count table using Samtools
... Hello, I need to generate a count table for my metagenomic data (10 samples), in an article which I referred it says. Count table can be generated using Samtools, can anyone validate me about this, and may I know whether I can find the command for the same in Samtools manual. Thanks, Vishal ...
assembly alignment written 5 months ago by vishalchanda36420 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: How to remove aligned sequnces?
... Thank You so much for the help. ...
written 5 months ago by vishalchanda36420
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How to remove aligned sequnces?
... Hello, I have been working on a metagenomic data, and now trying to remove ribosomal protein using the blastp command in BLAST+, I want to retain the sequences which **doesn't** map to the reference. Can anyone tell me how can I do that so that all the mapped sequences **Bacterial** gets removed and ...
alignment next-gen sequencing written 6 months ago by vishalchanda36420

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