User: devbt15

gravatar for devbt15
devbt1510
Reputation:
10
Status:
New User
Location:
Last seen:
3 months ago
Joined:
2 years, 9 months ago
Email:
d******@gmail.com

Posts by devbt15

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
940
views
1
answers
Comment: C: Bash: salmon command not found
... Any such package can be installed with the general command > conda install -c bioconda package but for some packages from repositories for Bioconductor package you have to link it to the uploader such as > conda install -c bioconda bioconductor-shortread One easy way is to google 'conda ...
written 14 months ago by devbt1510
0
votes
1
answer
1.1k
views
1
answers
Answer: A: RNA-seq DESeq2 : p-values and venn plots in same analysis
... As we cannot see the sample names it is hard to comment but I would presume that the order is same as in the text provided above. As such a heat map command would portray the absolute values from DESeq2 and here we can see that it is similar in both A and B in control and treatment respectively (It ...
written 20 months ago by devbt1510
0
votes
2
answers
1.5k
views
2
answers
Comment: C: HISAT2 index creation
... Dear Istvan, 1) Thank you for replying so promptly. I will surely try print commands to see if it yields something... 2) I did not get your suggestion of checking junctions variable at line 88? You mean splice junctions? 2) As for the file contents, I will try to paste first few columns of Lotus jap ...
written 2.3 years ago by devbt1510 • updated 2.3 years ago by Istvan Albert ♦♦ 82k
0
votes
2
answers
1.5k
views
2
answers
Comment: C: HISAT2 index creation
... Dear Istavan, Sure, the problem is the non-availability of .gtf files in our organism database and so I had to get it converted from .gff3 to .gtf. I have already tried this .gtf file with the usegalaxy.org server for RNA-Seq and it seems to work properly. **Here is a preview of my .gtf file c ...
written 2.3 years ago by devbt1510 • updated 2.3 years ago by Istvan Albert ♦♦ 82k
5
votes
2
answers
1.5k
views
2
answers
HISAT2 index creation
... Dear all, I am trying to create index file using the splice site and exon information from the .gtf file. However, using the hisat2 python commands in Ubuntu, I get empty output files. I verified hisat2 command with Saccharomyces gtf file and it produces respective files properly. In conclusion, I c ...
hisat2 rna-seq splice site index written 2.3 years ago by devbt1510
1
vote
1
answer
1.4k
views
1
answers
Comment: A: How to use 2 paired end .sam files in featureCounts?
... Yes, the hisat2 command should use both the fastq files in case of a paired end read sequencing. The resultant .bam file has to be put into featureCounts to get read counts for the features... ...
written 2.3 years ago by devbt1510
0
votes
3
answers
6.7k
views
3
answers
Answer: A: Insert Length Vs Nominal Length For Paired-End Data
... This page says that insert size is similar to nominal length: https://www.ebi.ac.uk/fg/annotare/help/seq_lib_spec.html Also the definition of nominal length on DDBJ Sequence Read Archive Handbook website (http://trace.ddbj.nig.ac.jp/dra/submission_e.html): Nominal Length*: Size of the insert for P ...
written 2.6 years ago by devbt1510

Latest awards to devbt15

Popular Question 14 months ago, created a question with more than 1,000 views. For HISAT2 index creation

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1041 users visited in the last hour