filter only for poly-X but nothing else

[avilella]

What would be the command-line to run AfterQC in order to filter only for poly-X reads but nothing else?

[sfchen]

Do you want to filter only polyG, or filter all of polyA/T/C/G?

[avilella]

all of polyA/T/C/G

On Wed, Dec 13, 2017 at 12:44 AM, Shifu Chen notifications@github.com wrote:

Do you want to filter only polyG, or filter all of polyA/T/C/G?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OpenGene/AfterQC/issues/31#issuecomment-351243801, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJpN-HRLOHZEgzVveKWmrf8YN8GMNsJks5s_x3egaJpZM4Q_IG5 .

[avilella]

Just to clarify, what I intend to do is to filter out the read pairs that look like polyA/T/C/G, but not trim or get rid of the reads that don't look like polyA/T/C/G but have low Q-scores or other issues.

[sfchen]

use following option to disable other trimmer / filters

-f0 -t0 -q0 -n1000 -s1000

[avilella]

Brilliant, thanks!

On Wed, Dec 13, 2017 at 10:08 AM, Shifu Chen notifications@github.com wrote:

use following option to disable other trimmer / filters

-f0 -t0 -q0 -n1000 -s1000

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OpenGene/AfterQC/issues/31#issuecomment-351344359, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJpN_TrHfAkdGGA9shdCfM0IubIYF-2ks5s_6ICgaJpZM4Q_IG5 .

[avilella]

I tried it with the command below, but it results in this:

# /home/avilella/AfterQC/after.py --no_overlap -f0 -t0 -q0 -n1000 -s1000 --read1_file=/home/avilella/CEGX_Run499/CEGX_Run499_enigma-12345678/CEG67_125_3-77840783/CEG67-125-3_S3_L001_R1_001.fastq.gz  --read2_file=/home/avilella/CEGX_Run499/CEGX_Run499_enigma-12345678/CEG67_125_3-77840783/CEG67-125-3_S3_L001_R2_001.fastq.gz --good_output_folder=/home/avilella/CEGX_Run499/CEGX_Run499_enigma-12345678/CEG67_125_3-77840783//afqc
Traceback (most recent call last):
  File "/home/avilella/AfterQC/after.py", line 228, in <module>
    main()
  File "/home/avilella/AfterQC/after.py", line 222, in main
    processOptions(options)
  File "/home/avilella/AfterQC/after.py", line 175, in processOptions
    filter.run()
  File "/home/avilella/AfterQC/preprocesser.py", line 773, in run
    self.addFiguresToReport(reporter)
  File "/home/avilella/AfterQC/preprocesser.py", line 788, in addFiguresToReport
    reporter.addFigure('Read1 per base discontinuity after filtering', self.r1qc_postfilter.discontinuityPlotly("r1_post_discontinuity", 'Read1 discontinuity curve after filtering'), 'r1_post_discontinuity', "")
  File "/home/avilella/AfterQC/qualitycontrol.py", line 234, in discontinuityPlotly
    json_str += "var layout={title:'" + title + "', xaxis:{title:'cycles'}, yaxis:{title:'discontinuity', range:" + makeRange(0.0, max(self.meanDiscontinuity)*1.5) + "}};\n"
ValueError: max() arg is an empty sequence

[avilella]

This is with 2x150bp pairs of fastq.gz files.

[sfchen]

Sorry, I made a mistake, it should be:

-f0 -t0 -q0 -n1000 -s0

[avilella]

I tested it and it works now. Thanks again for the prompt reply!