User: Shyam

gravatar for Shyam
Shyam120
Reputation:
120
Status:
Trusted
Location:
United States
Last seen:
3 weeks, 3 days ago
Joined:
4 years, 8 months ago
Email:
s********@yahoo.com

I am a PhD student working on next generation sequencing data. though I am a biologist, I work with both RNA-seq and whole genome sequencing data. I have experience with transcriptome de novo assembly, de novo assembly of whole genome and BAC clones data. Gene expression studies using the microarray data and rna-seq data were part of my dissertation. I have basic experience in perl, python languages, shell scripting. I am looking forward to improve my expertise in programming and new bioinformatics methods.

Posts by Shyam

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Small RNAseq data with untrimmed reads left after trimming process
... Where do these reads hit the genome? rRNA/tRNA? If the library prep is not good at the size fractionation you may get the fragmented rRNA/tRNA or other RNA classes might contaminate the library. If there is no 3' adapter in the reads, the insert might be longer than the 50 bp. You can do a BLAST at ...
written 24 days ago by Shyam120
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Answer: A: E-value results from hmmsearch are not accurate. [HMMER]
... For building a hmm from sequences you need to make a multiple sequence alignment first and use that alignment in fasta format as input for hmmbuild. If didnt align the sequences there is no way the resulting profile can predict any homology when you search back the input sequences. Hope this answers ...
written 10 months ago by Shyam120
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Comment: C: GATB-minia-pipelne fails at bloocoo step
... Its working now. I replaced the default bloocoo executable with the one I compile from the source and it is working now. Did the same for the minia too. ...
written 12 months ago by Shyam120
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Answer: A: Intall local BLAST in Ubuntu
... Most of the system requirements depend on the size of the database and the query and the blast program. From what I have seen blastx takes lot of time if the db and query sizes are big. Hope this gives you some idea. ...
written 12 months ago by Shyam120
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GATB-minia-pipelne fails at bloocoo step
... Hi: I am tryin g to install GATB-minia pipeline and the make went smoothly. When I run the test it fails at the bloocoo step with error Exception:[Errno 2] No such file or directory Evrything is as is with the git directory. I didn't change anything. /test folder is intact. Can anyone help w ...
gatb written 12 months ago by Shyam120 • updated 9 months ago by Ram17k
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Comment: C: bioperl MapTiling error
... I tried with different queries with different number of HSPs, it works if I use only the 'query' instead of 'subject' for my $sub_length_tiling = $tiling->length('subject'); I emailed Dr Jensen the developer for this module. Will update when I heard back from him. Thanks for the suggestio ...
written 18 months ago by Shyam120
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bioperl MapTiling error
... Hi I wrote a script for parsing blast output and get some of the statistics. But while I run the script: use strict; use warnings; use Bio::SearchIO; use Bio::Search::Tiling::MapTiling; my $infile = $ARGV[0]; my $in = Bio::SearchIO->new(-format => 'blast', -file = ...
bioperl blast written 18 months ago by Shyam120 • updated 13 months ago by Mark A. Jensen0
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Comment: C: How to calculate "fold changes" in gene expression?
... Can you direct to any references or studies used this method. thanks ...
written 18 months ago by Shyam120
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Comment: C: Fold change calculation
... I am not sure why there is a difference in your and the paper result. And they didn't mention log transformation. I think the value they gave is just FC. How you get the values you gave in your original post. Are they extracted from their analysis or you calculated them by yourself. The only thing I ...
written 2.3 years ago by Shyam120
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Answer: A: RPS Blast, COG and KOG analysis
... Hi Adrian: "Found COG and KOG databases here: ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/" Are these the updated KOGs. I didnt find any updates for the KOGs in the COG db ftp site ...
written 2.3 years ago by Shyam120

Latest awards to Shyam

Scholar 2.3 years ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: significant differential expressed gene validation
Autobiographer 2.3 years ago, has more than 80 characters in the information field of the user's profile.

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