User: Shyam

gravatar for Shyam
Shyam80
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80
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Location:
United States
Last seen:
2 months ago
Joined:
3 years, 5 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 • 26 results • page 1 of 3 • next >
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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 weeks ago by Shyam80
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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 9 weeks ago by Shyam80 • updated 7 weeks ago by Biostar ♦♦ 10
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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 12 weeks ago by Shyam80
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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 11 months ago by Shyam80
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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 11 months ago by Shyam80
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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 11 months ago by Shyam80
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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 11 months ago by Shyam80
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Comment: C: Data from the sequencing of the whole genome with LOW quality.
... I dont think I can help you there. As far as I now, very little percentage of reads contain adapter and low quality reads. Can't you simulate the data? ...
written 12 months ago by Shyam80
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Comment: C: Bioinformatics freelancers needed
... If you want us to trust you and your company, why couldnt you give the information on persons involved in this. If they are PhDs, lead us to their linked in profiles or publications etc. If you cant provide this info on your website, atleast you can post in on the social media. If you guys want us t ...
written 12 months ago by Shyam80
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Answer: A: Data from the sequencing of the whole genome with LOW quality.
... You can search the NCBI-SRA database for the larger data sets. But the quality info can only be retrieved if they report it in the related publication. Are you looking for data with adapter containg reads or the low phred quality score? You can check the recent Aegilops taushii, Triticum urartu or t ...
written 12 months ago by Shyam80

Latest awards to Shyam

Scholar 12 months ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: significant differential expressed gene validation
Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.

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