User: Shyam

gravatar for Shyam
Shyam80
Reputation:
80
Status:
Trusted
Location:
United States
Last seen:
1 day, 4 hours ago
Joined:
3 years, 9 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 • 29 results • page 1 of 3 • next >
0
votes
0
answers
96
views
0
answers
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 1 day ago by Shyam80
0
votes
6
answers
293
views
6
answers
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 1 day ago by Shyam80
0
votes
0
answers
96
views
0
answers
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 with th ...
gatb written 1 day ago by Shyam80
0
votes
1
answer
241
views
1
answers
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 6 months ago by Shyam80
0
votes
1
answer
241
views
1
answer
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 6 months ago by Shyam80 • updated 5 weeks ago by Mark A. Jensen0
0
votes
3
answers
58k
views
3
answers
Comment: C: How to calculate "fold changes" in gene expression?
... Can you direct to any references or studies used this method. thanks ...
written 6 months ago by Shyam80
0
votes
2
answers
6.7k
views
2
answers
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 15 months ago by Shyam80
0
votes
1
answer
2.6k
views
1
answers
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 15 months ago by Shyam80
0
votes
2
answers
6.7k
views
2
answers
Answer: A: Fold change calculation
... Fold change is calculated using - Test_read_count/Control_read_count For logFC, either get the actual FC and convert to log or convert the means of red count to log first and calculate logFC using log(test_mean) - log(control_mean) In your case, the log FC should be 1.8 (the log ratio column). ...
written 15 months ago by Shyam80
0
votes
2
answers
532
views
2
answers
Answer: A: question about Clip adapter in FASTX-toolkit for small RNA
... For smallRNA seq, you need to go with the reads with adapter clipped only. Any reads without the adapters are probably not the smallRNA because they are shorter than the read size (18 - 25nt) and read size is usually 50nt. The reads without any adapter sequences in them are most probably the degrade ...
written 15 months ago by Shyam80

Latest awards to Shyam

Scholar 16 months ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: significant differential expressed gene validation
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 764 users visited in the last hour