FASTQ files for Supplementary Table 4

[CDieterich]

Hi @lpryszcz

congratulations on your manuscript !

I would like to go through your analysis that produces STable 4. I have checked the EBI repository: https://www.ebi.ac.uk/ena/data/view/PRJEB55684 but there are no FASTQ files, only archives with FAST5 files.

Could you kindly share the FASTQ files for 3_NanotRNAseq_IVT+tRNAphe.tar.gz and 4_NanotRNAseq_IVT+tRNAphe.tar.gz with me ?

Thank you.

[MorghanLucas]

Hi Christoph!

I uploaded basecalled FAST5 files (so they contain FASTQ) - we thought that ENA would automatically extract the FASTQ, but it seems not to be the case. We contacted ENA about this but didn't hear anything yet, so I will upload the separate FASTQ files this week. Otherwise, you can download the FAST5 files (those runs are not so big) and extract the FASTQ.

Sorry for the inconvenience, and I will update you here when those FASTQs are publicly available.

Cheers!

[CDieterich]

Hi Lucas,

tried that in 4_NanotRNAseq_IVT nanopolish extract -o bla FAQ42155_3bd137b7_18.fast5

[extract] found 1 files, extracted 0 reads

Does not seem to work or am I doing something wrong ?

[lpryszcz]

Hi @CDieterich , please try fast5_to_fastq.py from https://github.com/lpryszcz/bin :

pip install ont_fast5_api
fast5_to_fastq.py -i workspace/*.fast5 | gzip > reads.fq.gz

For me it correctly retrieves FastQ reads from 4_NanotRNAseq_IVT+tRNAphe.tar.gz.

[CDieterich]

Hi @lpryszcz - thanks this worked for me.