User: Mohammad Heydarian

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100
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New User
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Last seen:
1 year, 5 months ago
Joined:
5 years, 9 months ago
Email:
m*******@jhmi.edu

Posts by Mohammad Heydarian

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Galaxy Pages - Importing/Downloading Embedded Data.
... Thanks so much, Jen! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 ...
written 4.3 years ago by Mohammad Heydarian100
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Galaxy Pages - Importing/Downloading Embedded Data.
... Hi All, Hope things are groovy. I am in the process of setting up a Galaxy page on the main server to host our NGS data. I am embedding the various datasets and they are showing up and viewable, but there is no way to import (or download) the data. Am I correct, or is the import button hidden on my ...
galaxy written 4.3 years ago by Mohammad Heydarian100 • updated 4.3 years ago by Jennifer Hillman Jackson24k
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Comment: C: Contents Of A Sam File
... Hi Benjy, To extract unmapped reads from a SAM file in Galaxy, you can use 'Filter SAM' ('NGS: SAM Tools' -> 'Filter SAM'). Add a 'flag' and use the 'The read is unmapped' type, then set the state for this flag to 'Yes'. This should return a SAM file with your unmapped reads. Cheers, Mo Heydar ...
written 4.3 years ago by Mohammad Heydarian100
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Answer: A: Exceptionally High Rpkm Values Of Mirna And Other Short Genes In Cuffdiff'S Outp
... Hi Thanh, This is due to Cuffdiff correcting for the size of smaller transcripts, the authors call it the "effective length correction". It is supposed to correct the loss of shorter transcripts upon size selection in creating your RNA-seq library. The default setting on Galaxy is to use the "effect ...
written 4.6 years ago by Mohammad Heydarian100
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Comment: C: Connecting To New Galaxy Cloudman By Ftp
... Hey Nate, Thanks for the response and instructions. I understand the last three steps of your protocol, but the first step is difficult for me to understand. I'm guessing that, "1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section", is telling me to change a setting o ...
written 4.6 years ago by Mohammad Heydarian100
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Connecting To New Galaxy Cloudman By Ftp
... Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and ...
galaxy written 4.6 years ago by Mohammad Heydarian100 • updated 4.6 years ago by Nate Coraor3.1k
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Comment: C: Cuffdiff Statistical Calculations Are Inconsistent?
... Hi Jeremy, The header of the Cuffdiff tool page says it is version 0.0.5 Is there a way, or setting, on Cuffdiff 2.0 to revert the parameters to be more similar to Cuffdiff 1.3? Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe ...
written 4.9 years ago by Mohammad Heydarian100
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Answer: A: Cuffdiff Statistical Calculations Are Inconsistent?
... We are having the exact same issue, on the main server and our (recent) cloud instances. Were some of the hidden Cuffdiff parameters modified since fall 2012? Cheers, Mo Heydarian ...
written 4.9 years ago by Mohammad Heydarian100
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Counting Rna-Seq Reads Per Class.
... Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cufflinks class codes ('=', 'j', 'u', 'x', etc...) and I am curious how others are determining how to count reads per class.. I tried first using the BedTools tool where you "count" the number of reads overla ...
bedtools cufflinks rna-seq written 5.4 years ago by Mohammad Heydarian100 • updated 5.4 years ago by Jennifer Hillman Jackson24k
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Cuffmerge - "Use Sequence" Option.
... Hi, Can anyone shed light on what the "use sequence" parameter (Y/N) in Cuffmerge is doing? The Cuffflinks manual says: -s/--ref-sequence / This argument should point to the genomic DNA sequences for the reference. When "no" is chosen for the "use sequence" option I still get genomic coordinates f ...
cuffmerge rna-seq written 5.8 years ago by Mohammad Heydarian100 • updated 5.8 years ago by Jeremy Goecks2.2k

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Popular Question 4.3 years ago, created a question with more than 1,000 views. For Cuffmerge - "Use Sequence" Option.

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