User: Shyam

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Shyam130
Reputation:
130
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Trusted
Location:
United States
Last seen:
4 months, 3 weeks ago
Joined:
6 years, 6 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 • 33 results • page 1 of 4 • next >
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Answer: A: to calculate coverage of each contig after assembly
... Bowtie and Tophat are short read aligners. Though tophat support longer reads like from 454 it has a limit of 1024 bases. BWA-MEM is a better option for alignment and you can get the coverage stats using samtools. I assume the 454.10species.fasta is the read file. You need to us the multi-fasta file ...
written 5 months ago by Shyam130
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Answer: A: Quality and length trimming for de novo assembly of RNAseq
... First of all, use FastQC to look at the quality of Data. FastQC website has examples of good and bad data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ . Only trim the 3' side of the read (right hand side) if the data is bad. Check if there is adapter contamination. You can use tools ...
written 5 months ago by Shyam130
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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 22 months ago by Shyam130
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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 2.6 years ago by Shyam130
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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 2.8 years ago by Shyam130
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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 2.8 years ago by Shyam130
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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 2.8 years ago by Shyam130 • updated 2.5 years ago by RamRS27k
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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 3.3 years ago by Shyam130
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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 3.3 years ago by Shyam130 • updated 2.9 years 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 3.3 years ago by Shyam130

Latest awards to Shyam

Teacher 22 months ago, created an answer with at least 3 up-votes. For A: significant differential expressed gene validation
Scholar 4.1 years ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: significant differential expressed gene validation
Autobiographer 4.1 years ago, has more than 80 characters in the information field of the user's profile.

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