User: Sammy

gravatar for Sammy
Sammy10
Reputation:
10
Status:
New User
Location:
Last seen:
5 days, 15 hours ago
Joined:
1 year, 4 months ago
Email:
r*********@gmail.com

Posts by Sammy

<prev • 28 results • page 2 of 3 • next >
0
votes
1
answer
982
views
1
answers
Comment: A: .slurm vs .sh files
... Thanks. So I have different types of shells: C shell (#!/bin/csh); BASH (#!/bin/bash); Korn shell (#!/bin/ksh) etc... But BASH does not need a suffix like .sh or .csh. (Should it be .bash?) You use SLURM to interact with HPC to run your script (written in BASH or Bourne Shell (.sh)). You can mark t ...
written 11 months ago by Sammy10
9
votes
1
answer
982
views
1
answer
.slurm vs .sh files
... Hello. I am writing my first ever script. Is there any difference between somefile.slurm and somefile.sh? Are both terminologies human convention? I know that you can use them both to submit jobs but I don't understand the practical differences between them (if there is any). Thanks. ...
rna-seq written 11 months ago by Sammy10
0
votes
0
answers
216
views
0
answers
Comment: C: GSM records without a corresponding SRA
... No, there are raw data available in the GSM. I am looking for RNA-seq from the 3rd party to process. Sometimes the SRP series is not as easy to find but I get it most of the times. The thing is that I upload the samples directly into Galaxy with the SRP. I don't really know what to do just with the ...
written 13 months ago by Sammy10
0
votes
0
answers
216
views
0
answers
GSM records without a corresponding SRA
... Hey, By your knowledge, is there possible for GSM records to not have a corresponding SRA page? ...
rna-seq written 13 months ago by Sammy10
0
votes
0
answers
278
views
0
answers
(Closed) TopHat and HISAT2
... Hey, all. Why TopHat gives totally different alignments when I change the Library Type (First strand vs. Second strand) and for HISAT2 the alignments are pretty much the same (Reverse vs. Forward). I am trying to read the papers that describes them but so far, couldn't explain this. I am aware of ...
rna-seq written 14 months ago by Sammy10
0
votes
0
answers
749
views
0
answers
Comment: C: Hisat2 vs. TopHat vs.Bowtie2
... Got it. Just to make sure for future references because I am new here and I kind of training myself in bioinformatics talking with very few people about it (so I really have to learn the terminology better): I am using Galaxy. Should I specify the function used and the chosen option? I am not sure a ...
written 14 months ago by Sammy10
0
votes
0
answers
353
views
0
answers
Comment: C: Library Types in TopHat and Hisat2
... Great. Thanks. So what you are saying is that I should not take the results from TopHat into consideration. ...
written 14 months ago by Sammy10
2
votes
0
answers
353
views
0
answers
Library Types in TopHat and Hisat2
... Hey, Does anyone know how to explain the background process on how spliced aligners (Hisat2, TopHat) use Library Types (Second Strand/ First Strand, Forward/Reverse respectively) to align the reads to the genome? More specifically, how Library Types influence the alignment. I am trying to understa ...
rna-seq written 14 months ago by Sammy10
0
votes
0
answers
749
views
0
answers
Comment: C: Hisat2 vs. TopHat vs.Bowtie2
... Right, but what about TopHat and Hisat2. Why Hisat2 gives me exons that are that long in comparison to TopHat when I introduce the same Library Type as an options (well, in this case the equivalent). I should add that I get long exons in TopHat as well but when I choose First Strand or Unstranded an ...
written 14 months ago by Sammy10
0
votes
1
answer
692
views
1
answers
Comment: C: Merging SAM/BAM files
... Huh. Probably because I don't think I know what you mean by that. Can you please give me more details? I am intrigued. ...
written 14 months ago by Sammy10

Latest awards to Sammy

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1906 users visited in the last hour