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GuoBioinfoLab / CATT

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.
http://bioinfo.life.hust.edu.cn/CATT/
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Chromium 10X #10

Open SaraValpione opened 4 years ago

SaraValpione commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

Hi @SaraValpione,

thanks, would very much appreciate that!

Best, Ben