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It does not seem to recognize Tcongo_L003_R2_001.fastq.gz and Tcongo_L003_R1_001.fastq.gz files. When I tried to give paths to each of these, I get the same error below.
!!!!! WARNING: Could not ls Tcongo_1_TCO_S1_L003_R2_001.fastq.gz
EXITING: because of fatal INPUT file error: could not open read file: Tcongo_1_TCO_S1_L003_R2_001.fastq.gz
SOLUTION: check that this file exists and has read permision.
Some help please.
The text was updated successfully, but these errors were encountered:
I am trying to align single cell RNA-data set using using STAR and following the manual. I however can't get this to run.
STAR --runThreadN 10 --genomeDir ./T_congoSc/Tcongo_noUTR-index
--readFilesIn ./Tcongo_scell/Tcongo_L002_R2_001.fastq.gz,Tcongo_L003_R2_001.fastq.gz ./Tcongo_scell/Tcongo_L002_R1_001.fastq.gz,Tcongo_L003_R1_001.fastq.gz
--outFilterScoreMin 30 --clipAdapterType CellRanger4 --soloType CB_UMI_Simple --soloCBstart 1 --soloUMIstart 17 --soloCBlen 16 --soloUMIlen 12 --soloBarcodeReadLength 0
--soloCBwhitelist ./barcodes/3M-february-2018.txt --soloUMIdedup 1MM_CR
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR
--outFileNamePrefix ./mapping_stats/Tcongo_2
--soloMultiMappers EM --soloFeatures Gene --readFilesCommand zcat --soloCellFilter EmptyDrops_CR
It does not seem to recognize Tcongo_L003_R2_001.fastq.gz and Tcongo_L003_R1_001.fastq.gz files. When I tried to give paths to each of these, I get the same error below.
!!!!! WARNING: Could not ls Tcongo_1_TCO_S1_L003_R2_001.fastq.gz
EXITING: because of fatal INPUT file error: could not open read file: Tcongo_1_TCO_S1_L003_R2_001.fastq.gz
SOLUTION: check that this file exists and has read permision.
Some help please.
The text was updated successfully, but these errors were encountered: