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CIT files from BAM files generated using STAR solo #4

Open aishwarya-gondane opened 6 months ago

aishwarya-gondane commented 6 months ago

Hi,

I have scSLAM-seq from two samples (control, treated). I have aligned the fastq file using STAR Solo and now trying to generate the CIT file from the Bam files. I will next use the CIT in GRAND-SLAM and then in GRANDR.

I have encountered below error WARNING Did not find filtered barcodes for Control_STAR_solo_alignedAligned.sortedByCoord.out.bam!

Command: /media/volume_scSLAMseq/GRAND-SLAM_2.0.7b/gedi -e Bam2CIT -p -10x Control_NVP_scSLAM_STARSolo_10x.cit Control_STAR_solo_alignedAligned.sortedByCoord.out.bam N_STAR_solo_alignedAligned.sortedByCoord.out.bam

I am not sure if I should add the paths to the barcodes files after "-10x" argument?

Thanks, Aish.

florianerhard commented 6 months ago

Dear Aish. you are using a still experimental feature! We have tested bam2cit with both CellRanger outputs as well as STARsolo outputs (with matching to Cellranger results. You have to make sure that bam2cit finds the barcodes.tsv file generated by STARsolo (in the fitered folder). It looks at several places, the easiest would be to put it next to the bam file and name it filtered_barcodes.tsv)!

Florian

theheking commented 2 months ago

Hi Florian, I was wondering if there was any other expansions or documentation of this experimental feature? Cheers, Helen