Chromium 10X

[SaraValpione]

Hi, congratulations for the project, great job.
I have some questions regarding the analysis of Chromium 10X format data.

From the documentations:
catt --tenX --f1 R1 --f2 R2 -o outputName

Chromium 10X output consists of 6 FASTQ files split into two sequencing lanes L001 and L002, each with 2 reads of R1 (barcodes), R2 (cDNA sequences), I1 (illumina lane info); are catt R1 and R2 argument operators for the script or shall I substitute them with the 2 + 2 *.fastq.gz file names? If this is the case, what syntax please? I have tentatively tried to run (from the folder where I have the 6 FASTQ files)

catt --tenX --f1 R1 --f2 R2 -o outputName

and also

catt --tenX --f1 sample_L001_R1_001.fastq.gz --f2 sample_L001_R2_001.fastq.gz -o outputName

but in both cases I have the following error message:

Program start
ERROR: LoadError: MethodError: no method matching split(::Array{String,1}, ::Char)
Closest candidates are:
split(::T, ::AbstractChar; limit, keepempty) where T<:AbstractString at strings/util.jl:387
split(::T, ::Any; limit, keepempty) where T<:AbstractString at strings/util.jl:379
split(::CategoricalValue{String,R} where R<:Integer, ::Any; kwargs...) at deprecated.jl:70
Stacktrace:
[1] split_10X(::Array{String,1}, ::Array{String,1}) at ./CATT/catt.jl:634
[2] proc(::Dict{String,Any}) at ./CATT/catt.jl:721
[3] top-level scope at ./CATT/catt.jl:806
[4] include(::Function, ::Module, ::String) at ./Base.jl:380
[5] include(::Module, ::String) at ./Base.jl:368
[6] exec_options(::Base.JLOptions) at ./client.jl:296
[7] _start() at ./client.jl:506
in expression starting at ./CATT/catt.jl:805

Any suggestions to resolve this issue please?
Thank you in advance for your help!

Sara

[b-schubert]

Has there been any progress on this issue? I am also trying to run CATT on some 10X samples and get the same error.

Thanks for your help,
Ben

[SaraValpione]

Hi, I developed a custom pipeline... I am still parsing it but seems running, will keep you in the loop if it works!
BW

Sara

[b-schubert]

Hi @SaraValpione,

thanks, would very much appreciate that!

Best,
Ben