Path of the fastq

[parsboy66]

Thanks for a nice tool!

i used sc tagger to read the fastq from the path( there are 1000 fastq in 1 path). it seems sctagger needs directly a fastq as input not the path, is that right? and if so, how can i pass a path of fastqs to sctagger?

error: IsADirectoryError: [Errno 21] Is a directory: '/fastq_pass'

Thanks Iman

[baraaorabi]

Hello Iman,

I think you have two options.

• The --reads takes multiple arguments. So you can pass all FASTQ paths comma separated.
• You can create a UNIX pipe to concatenate all the FASTQs on the fly (without having to use disk storage). This would be somehthing like:

scTagger.py extract_lr_bc --reads <(cat PATH/TO/FASTQ/DIRECTROY/*.fastq)