some question about using scisorseqr

[yuanwsy]

Hi,Thanks for developing such a good tool!
When I am using the getbarcodes step ,I use the following command:
GetBarcodes(fqFolder = fastqFolder, BCClustAssignFile = bc_clust, outputFolder="/data/R02/yuanwsy/scisorseqr/scisorseqresult/",
chemistry = "v3", concatenate = TRUE, filterReads = FALSE)

and the bc_clust looks like this ,the same as the example

V1	V2
TCGCAGGGTGTCATTG	Macrophage
CTTGATTGTGTTCGTA	Pericyte
NA	NA
TACATTCAGCCAACCC	B cell
ATTCGTTGTGCCGTAC	iOSN
TAGGTACAGAGCCGAT	B cell
CATCCGTCAAGTCATC	HBC
CAGCGTGCAAGTACCT	Neutrophil

but after I ran the command line ,It came to an error like this:
cat: ./OutputRaw//DeconvBC*.csv: No such file or directory

I can not find the the information of DeconvBC*.csv in the vignette ,do you know how to solve it?
Thanks!

[noush-joglekar]

Hey - it seems that it is not finding the correct output files for concatenating the results. Are you getting any files in the OutputRaw folder? What do they look like?

[yuanwsy]

after I ran the command ,It generated two folders：outputraw and outputfilter
the outputraw is empty,and the outputfilter contains a file named FilteredDeconvBC_AllFiles.csv

[noush-joglekar]

Huh, so it seems it is not really running the program at all. Does it print the name of the fastq files in the folder when you run the command?

[lhmaniero]

Hi @noush-joglekar ,

I’m getting the same issue.

Please, see what’s going on:

#I’ve use this command to run “GetBarcodes”
scisorseqr::GetBarcodes(fqFolder = fastq, BCClustAssignFile = barcode, output_dir, 6, "v3.1", concatenate = TRUE, filterReads = FALSE)

#Error message
cat: '/path_to_my_output_folder//OutputRaw//DeconvBC*.csv': No such file or directory

Then, it creates two folders in my output_folder (see image below):

Lastly, when I opened the folder OutputFiltered, it created this file: "FilteredDeconvBC_AllFiles.csv". File is empty.

#I also tried to run again, without deleting the folders inside the output_dir, see the error message:

cat: '/path_to_my_output_folder/OutputRaw//DeconvBC*.csv': No such file or directory
Warning message:
In dir.create(filt_Output) :
'/path_to_my_output_folder/OutputFiltered' already exists

Any thoughts? Could you help instructing how to solve this issue?

Thanks in advance for your time and support (:

By the way, it did not print the name of the fastq files in the folder when I’ve ran the command.

[noush-joglekar]

Hey! Could you try with chemistry = "v3" instead of "v3.1" and also perhaps show me a head of your barcode file?

[lhmaniero]

Hey! Could you try with chemistry = "v3" instead of "v3.1" and also perhaps show me a head of your barcode file?

Here it is:
I followed the example as described here: https://github.com/noush-joglekar/scisorseqr/blob/master/vignettes/scisorseqr-StandardWorkflow.pdf

Head picture as you requested:

I also changed the parameter for “v3” as you mentioned and got the same error, see bellow:

cat: './OutputRaw//DeconvBC*.csv': No such file or directory
Warning message:
In dir.create(filt_Output) : './OutputFiltered' already exists

It created the folders and the empty file as mentioned before.

Thanks again @noush-joglekar (:

[noush-joglekar]

Ah, could you remove the "1" from the end of the barcodes? And also I don't think it matters but the spaces in the cell type labels could cause issues down the line