multiqc hisat2 transfer

Question

[smithkthedale]

Hello,

I have my hisat2 files in an error folder hisat2_16132589.err

[dalesmith@outputRNAAqSeq]$ cat hisat2_16132589.err 65922241 reads; of these: 65922241 (100.00%) were paired; of these: 26359865 (39.99%) aligned concordantly 0 times 37456235 (56.82%) aligned concordantly exactly 1 time

2106141 (3.19%) aligned concordantly >1 times
----
26359865 pairs aligned concordantly 0 times; of these:
  5633201 (21.37%) aligned discordantly 1 time

How do I take all of these files and convert them to multiqc files? I know the command multiqc . but don't know how to get all of the hisat2 files to be processed as multiqc. What would the script be?

[Matthias Zepper]

MultiQC aggregates log files using search patterns specified in search_patterns.yaml. For HISAT2 files, it looks for a text snippet corresponding to HISAT2 summary stats:.

As long as this shibboleth is part of your log files, it should process them normally. Just specify the path to the folder containing your log files. If you wish to restrict MultiQC to the HISAT2 Module, use the -m parameter.

[smithkthedale]

Can you help me fix my script?

[Matthias Zepper]

Which script? You don't need a script. You just need to run multiqc /path/to/your/logfilefolder -m hisat2.

If your log files like hisat2_16132589.err contain the line "HISAT2 summary stats:", MultiQC will detect them automatically.