User: Shyam

gravatar for Shyam
Shyam100
Reputation:
100
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Trusted
Location:
United States
Last seen:
1 month, 2 weeks ago
Joined:
4 years 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 • 30 results • page 1 of 3 • next >
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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 7 weeks ago by Shyam100
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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 3 months ago by Shyam100
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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 3 months ago by Shyam100
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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 3 months ago by Shyam100 • updated 4 weeks ago by Ram12k
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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 9 months ago by Shyam100
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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 10 months ago by Shyam100 • updated 5 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 10 months ago by Shyam100
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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 19 months ago by Shyam100
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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 19 months ago by Shyam100
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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 19 months ago by Shyam100

Latest awards to Shyam

Scholar 20 months ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: significant differential expressed gene validation
Autobiographer 20 months ago, has more than 80 characters in the information field of the user's profile.

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