User: devbt15

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devbt1510
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Posts by devbt15

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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 11 days ago by devbt1510
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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 7 months ago by devbt1510 • updated 7 months ago by Istvan Albert ♦♦ 77k
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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 7 months ago by devbt1510 • updated 7 months ago by Istvan Albert ♦♦ 77k
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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 7 months ago by devbt1510
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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 7 months ago by devbt1510
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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 10 months ago by devbt1510

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