Multiple fastq files (multiple samples)

[gk-bioin4m8x]

Hi @LuyiTian,
I have run your tutorial https://bioconductor.org/packages/devel/bioc/vignettes/scPipe/inst/doc/scPipe_tutorial.html and has been successful. However, I am wondering if I have multiple fastq files (multiple samples), how would I start as well as find the read_structure? I have used "get_read_str" but getting error that:
could not find function "get_read_str"
Please guide.
Thanks.

[gk-bioin4m8x]

@LuyiTian Any updates please?

[gk-bioin4m8x]

@LuyiTian Any updates please?

[mritchie]

Sorry for the delay in replying. @Shians who wrote the get_read_str function is away on holidays at the moment. The function is new and not exported, so to access, try scPipe:::get_read_str. It currently supports a few known formats we've encountered, so may not work if your data is in a format we haven't seen.
To deal with multiple fastq files (1 per sample) perhaps try concatenating them before running.

[LuyiTian]

please check the document in sc_exon_mapping. it accepts multiple bam files, each representing a cell. you need to set bc_len to 0 and provide a barcode_vector like c("CELL001","CELL002","CELL003"). the elements in the barcode vector should be the same length.

if you do this, you also need to set max_mis=0 in other functions to disable the fuzzy search。

Sorry, this is a recently added function and we haven't included them in the tutorials yet.

scPipe is still under active development so it is recommended to use the dev version of scPipe to have the recent updations and new features.

[gk-bioin4m8x]

Thanks @mritchie @LuyiTian I will try again.