Does MToolBox have been tested on FASTQ coming from the Ion Proton Sequencing Platform ?

[3i-v]

I used to analyse FASTQ files coming from the PGM system (ThermoFisher); Often, Mtoolbox failed on 1 sample at least ; and I am not able to solve the issue except when eliminating some reads from the FASTQ (trial and error approach). The MtoolBox analysis applied on the rest of the samples and coming from the same chip works well. Today I try to analyse a new batch of samples sequenced on the Ion Proton Sequencing Platform. This time, the MToolbox analysis failed on the 3 first samples tested. So, I am wondering if the FASTQ coming from the Ion Proton system are Mtoolbox compatible. Do some MToolBox users succeed to analyse FASTQ files coming from the Ion Proton system or do I am the only one where the MtoolBox analysis failed ? Thank you for your feedback. Regards

[clody23]

Hi, we didn't test MToolBox on IonProton sequences yet, but it would be good to check if it is compatible with that technology.

What is the average length of the reads you're working with?

Also would be useful to have a log file with the stderror of one of these processes to be able to understand where the pipeline fails.

Best, Claudia

[3i-v]

Hi Claudia, First I am so sorry of my late answer. Here it is.

Again I have tested recently a sample that previously failed, and I did not obtain a sucess in the analysis. The FASTQ I analyse is coming from a PGM platform. The average length of the reads is 205

The log file I obtain is attached to this post. I masked some 'critical' info with xxxx and (...)

If it is easier for you to test what's going wrong with the file I am ready to share this FASTQ file IonXpress_081.fastq with you. Let me know how I can transfer the file to you (size: 56M).

Again, 95% of my samples sequenced on the PGM succeeded in the analysis but 5% failed. I can sent you a second FASTQ to make the test on your side. MToolBox_IonXpress_081.log

Thank you very much,