Trimming quality step dropping all reads

[safinaARK]

Dear Ivan,

I want to know that how can i skip the step of trimming as this step is dropping all of my fastq reads or how can i make changes in the trailing and leading parameters of the trimming step? As many of my samples after trimming step generating empty clean-read files.

Thanks
SAR

[GunzIvan28]

Hey @safinaARK,
To be reasonable and inclusive, I had created a Q-score of 27 and minimum read length of the final trimmed reads by default within the pipeline. Now if your reads fall below these set limits, that could explain why your reads are being dropped so it is likely that you very poor quality reads in your sequences.

At this point, I am interested in knowing the quality metrics for your reads (kindly share your fastqc and multiqc results located in $OUTPUT/reports/quality_stats). It is from these that I will advise you on the parameters to change line per line within the pipeline.

BUT A PRIOR WARNING:
During the testing and compilation of the pipeline, we deduced that the default set parameters were sufficient to produce credible results. We as the authors can not guarantee the authenticity of the results that will be generated after lowering these said parameters. However, we can proceed with setting and modifying the parameters to fit your data sets.

I will await your feedback.

Ivan

[safinaARK]

Dear

Hey @safinaARK, To be reasonable and inclusive, I had created a Q-score of 27 and minimum read length of the final trimmed reads by default within the pipeline. Now if your reads fall below these set limits, that could explain why your reads are being dropped so it is likely that you very poor quality reads in your sequences.

At this point, I am interested in knowing the quality metrics for your reads (kindly share your fastqc and multiqc results located in $OUTPUT/reports/quality_stats). It is from these that I will advise you on the parameters to change line per line within the pipeline.

BUT A PRIOR WARNING: During the testing and compilation of the pipeline, we deduced that the default set parameters were sufficient to produce credible results. We as the authors can not guarantee the authenticity of the results that will be generated after lowering these said parameters. However, we can proceed with setting and modifying the parameters to fit your data sets.

I will await your feedback.

Ivan

Dear Ivan,

Thank you for your response,
Please find the quality stats:

multiqc_fastqc.txt

Thanks

SAR

[GunzIvan28]

@safinaARK,
Thanks for sharing the file. However this is not sufficient for me to deduce what parameters to adjust. Kindly share the interactive html multiqc report or the html fastqc reports for the samples

Thanks
Ivan

[safinaARK]

Dear
quality_reports.zip
@GunzIvan28,

Im sharing the html reports for those samples whose assemblies were not generated:

quality_reports.zip

Thanks

[GunzIvan28]

@safinaARK
Thanks for the file. From what i see, all your sequences have a q-score above 30. SO the reason why they are being dropped on trimming is that the sequence lengths prepared in the library were 75bps long while rMAP's minimum trimming length is 80bps.

So here is the simplest work around i can suggest:
Access the rMAP script located at $HOME/miniconda3/envs/rMAP-1.0/bin/rMAP using you test editor and change line 28 which has MINLEN=80 to MINLEN=30 and then run the pipeline again. Let me know how it goes.

Cheers,
Ivan

[safinaARK]

@GunzIvan28
I have updated the script and have started the analysis will update you once this is complete.

Thanks

SAR

[safinaARK]

@GunzIvan28

Superb! .. It is now working

Thanks

SAR

[GunzIvan28]

Great thanks for the feedback.

Cheers,
Ivan