Tophat 2 error

Question

[priteshrhsabara]

Error: could not open writer pipe gzip -cf - < /home/orf8/Desktop/mirna/nc/tmp/left_kept_reads.m2g_um_seg508.fq.z

[mittu1602]

Sorry this query is not understandable could you elaborate what are you trying to do?

[WouterDeCoster]

Hi priteshrhsabara,

This question needs a lot more information, please elaborate, how do you expect us to solve your problem if this is all you write?

In addition (based on your title), you should know that the old 'Tuxedo' pipeline of Tophat(2) and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

Cheers,
Wouter

[GenoMax]

Is the disk you are trying to write to full or close to?