Results

This pipeline generates several result tables, sequence lists and a report in LaTeX.

Outputted files

Tab separated files with raw read counts:

• Counts of Novel sequences only

  • novel=${workdir}/count/all_seq_counts_novel.tsv

• Counts of filtered reads

  • noncons=${workdir}/count/all_seq_counts_nonCons.tsv

• Counts of Tasi sequences only

  • tasi=${workdir}/count/all_seq_counts_tasi.tsv

• Counts of simultaneously Novel and Tasi sequences only

  • novelTasi=${workdir}/count/all_seq_counts_novelTasi.tsv

• Counts of conserved sequences only

  • cons=${workdir}/count/all_seq_counts_cons.tsv

• Merge of all counts together

  • reunion=${workdir}/count/all_seq.tsv

Files with lists of sequences:

• List of conserved sequences only

  • consSeq=${workdir}/count/all_seq_cons.seq

• List of sequences that have been identified as a star sequence

  • star=${workdir}/count/all_seq_star.seq

• List of Novel sequences only

  • novelSeq=${workdir}/count/all_seq_novel.seq

• List of Tasi sequences only

  • tasiSeq=${workdir}/count/all_seq_tasi.seq

• List of simultaneously Novel and Tasi sequences only

  • novelTasiSeq=${workdir}/count/all_seq_novelTasi.seq

Temporary files that are created and removed during execution:

• Temp file to store novel sequences

  • novelTmpSeq=`mktemp /tmp/novelSeq.XXXXXX`

• Temp file to store novel counts

  • novelTmp=`mktemp /tmp/novel.XXXXXX`

• Temp file to store tasi sequences

  • tasiTmpSeq=`mktemp /tmp/tasiSeq.XXXXXX`

• Temp file to store tasi counts

  • tasiTmp=`mktemp /tmp/tasi.XXXXXX`

Other files of interest are located in:

• Files related with precursor prediction (miRCat)

  • ${workdir}/data/mircat

• Files related with tasi prediction

  • ${workdir}/data/tasi

Report

The report is written in LaTeX and is ready to be converted to pdf. However to keep this pipeline light Tex Live is not included and therefore should be installed to convert it to pdf. Most package managers include these tools so this shouldn’t give you a hard time.

The tex file is written to:

• ${workdir}/count/miRPursuit_REPORT-Run[PPID].tex

To convert to pdf once Tex Live package is installed. Note that other dependencies might be needed::

texi2pdf ${texfile}