User: ashis.csedu

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ashis.csedu80
Reputation:
80
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United States
Last seen:
7 months, 1 week ago
Joined:
7 years, 7 months ago
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a**********@gmail.com

I'm a first year PhD student trying to analyze data from RNA-seq experiments!

Posts by ashis.csedu

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How To Convert Bigwig To Bam?
... Thanks for clarifying the mis-understanding. It helps. ...
written 7.4 years ago by ashis.csedu80
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How To Convert Bigwig To Bam?
... I am working with some bigwig data that were generated from bedGraph data from an RNA-seq experiment. Since the bigwig files I have list coverage scores with 1bp span. These bigwig/bedGraphs were generated from BAM files that I don't have, but can I re-create those BAM files from BigWigs? Thanks. ...
bam bigwig written 7.4 years ago by ashis.csedu80 • updated 7.4 years ago by Jorge Amigo11k
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Comment: C: How To Get The The Ncrna Loci From Ucsc Genome Browser Downloads
... Much elaborate workflow to get ncRNAs! Thanks Vikas Bansal. ...
written 7.4 years ago by ashis.csedu80
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Comment: C: How To Get The The Ncrna Loci From Ucsc Genome Browser Downloads
... Thanks Wjeck. I got that by looking at the CDS positions. Really helps. ...
written 7.4 years ago by ashis.csedu80
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How To Get The The Ncrna Loci From Ucsc Genome Browser Downloads
... Hi, I am looking for ncRNA loci after reading a paper where the authors stated that they collected the ncRNA loci from the UCSC genome Browser. I've been looking for it in the download section and also in the Table browser. Can you help me to find out that (for example a sample specis: Mouse (mm9)? ...
mouse written 7.4 years ago by ashis.csedu80 • updated 7.4 years ago by Vikas Bansal2.4k
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Comment: C: What Is The Total Size Of Hgdownload.Cse.Ucsc.Edu/Gbdb/Mm9
... I just got the answer by using the "rsync" command: rsync --size-only --recursive rsync://hgdownload.cse.ucsc.edu/gbdb/mm9/ And the answer is, currently (today 1 July, 2012, 1:50PM UTC-5), the total size of that directory is 726.6236514812 GB that includes 1256 files in it. Thanks anyway. ...
written 7.4 years ago by ashis.csedu80
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What Is The Total Size Of Hgdownload.Cse.Ucsc.Edu/Gbdb/Mm9
... Hi, I was mirroring the UCSC genomebrowser in Ubuntu 12.04 following the steps mentioned in http://enotacoes.wordpress.com/2009/09/03/installing-a-minimal-ucsc-mirror-in-ubuntu-jaunty-64-bits/. The very last step was to download the "gbdb" data using the command: rsync -avzP --delete --max-delete=2 ...
ucsc written 7.4 years ago by ashis.csedu80 • updated 7.4 years ago by Istvan Albert ♦♦ 81k
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Comment: C: Tophat Protocol Error Occured At Step 4
... Thanks for your answer. I looked for the headers in the "genome.fa" and got 7 sequences having headers - 2L,2R,3L,3R,4,M,X. And also I looked in to the "gene.gtf" and found that 46265 entries have header "2L", but only 89 "2LHet". Similarly, there are 60521 "2R" entries, and 470 "2RHet" entries. Cuf ...
written 7.5 years ago by ashis.csedu80
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Tophat Protocol Error Occured At Step 4
... Hi all, I was doing differential gene and transcript expression analysis by following the Tophat protocol (published in Nature protocol in March 2012) on the same example D. melanogaster as it is mentioned in the paper. But I am confused of an error/warning message at step 4: Running Cuffmerge on al ...
tophat rna-seq written 7.5 years ago by ashis.csedu80 • updated 4.7 years ago by jhluo21660
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Comment: C: Is This Always The Case That The Wig/Bigwig/Bed Files Are Meant Only For Viewing
... Thanks for the information. ...
written 7.6 years ago by ashis.csedu80

Latest awards to ashis.csedu

Great Question 2.4 years ago, created a question with more than 5,000 views. For Tophat Protocol Error Occured At Step 4
Great Question 2.4 years ago, created a question with more than 5,000 views. For How To Get The The Ncrna Loci From Ucsc Genome Browser Downloads
Great Question 2.4 years ago, created a question with more than 5,000 views. For How To Convert Bigwig To Bam?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For How To Get The The Ncrna Loci From Ucsc Genome Browser Downloads
Popular Question 5.2 years ago, created a question with more than 1,000 views. For How To Convert Bigwig To Bam?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Tophat Protocol Error Occured At Step 4
Popular Question 5.9 years ago, created a question with more than 1,000 views. For How To Get The The Ncrna Loci From Ucsc Genome Browser Downloads
Popular Question 5.9 years ago, created a question with more than 1,000 views. For How To Convert Bigwig To Bam?
Autobiographer 5.9 years ago, has more than 80 characters in the information field of the user's profile.

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