gene_transposon_cluster_direct_mapping is absent from piPipes rna output

[blaiseli]

The documentation for the RNA-Seq pipeline (https://github.com/bowhan/piPipes/wiki/RNA-seq) mentions a gene_transposon_cluster_direct_mapping directory that is not present in the output of piPipes rna.

[bowhan]

I will need more information to debug. Can you please run piPipes_debug (instead of piPipes) in a new, clean directory and attach the stdout and stderr? Thank you!

[blaiseli]

Hi,

I ran using piPipes_debug as you suggested.

You can find the logs here: stdout: http://www.normalesup.org/~bli/cn_bw_piPipes_rna.log stderr: http://www.normalesup.org/~bli/cn_bw_piPipes_rna.err

The output directory contains the following:

rRNA_mapping/
input_read_files/
cn_bw_.basic_stats
cufflinks_output/
bigWig/
htseq_count/
genome_mapping/
pdfs/
direct_transcriptome_mapping/

Hope this helps.

[bowhan]

Actually gene_transposon_cluster_direct_mapping has been replaced by direct_transcriptome_mapping so you are fine. The Wiki needs to be updated. And "cluster" has been removed from the transcriptome index (leaving only gene mRNA and transposon consensus sequences). The reason to use consensus sequence is to avoid multi-mappers and incorporating cluster sequences is against this purpose. Plus, there is little evidence that dual-strand clusters are transcribed as a whole.