Hello, I have a folder called ~/pooled that contains 12 folders with 12 different names, e.g. bristol, altadena, hermanville, taunton. Each of these 12 folders contains a Log.final.out file output from STAR containing alignment statistics. I would like to run the multiQC software on all 12 log files in this way: multiqc output/alignment/reference/star/pooled/*/Log.final.out (1) or in this way: multiqc --file-list output/alignment/reference/star/pooled/pathsToLogFinalOut.txt (2) The file pathsToLogFinalOut.txt contains the paths to each of the log files. However, in both cases only one of the log files is analysed. The first command (1) only outputs the results for hermanville. The second command (2) only outputs results for taunton.
It's odd because the HTML file shows that the report was generated using data in:
Report generated on 2016-10-14, 14:10 based on data in:
~/pooled/bristol/Log.final.out ~/pooled/altadena/Log.final.out ~/pooled/taunton/Log.final.out ~/pooled/hermanville/Log.final.out
Can someone help me, please?