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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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cellranger count: ERROR : --transcriptome NO such file or directory #113

Closed MubasherMohammed closed 3 years ago

MubasherMohammed commented 3 years ago

Hi, I run into ERROR while using cellranger count function for genome alignment and its "NO such file or directory" for the transcriptome I couldn't figure it out as I make sure the path is correct

command

cellranger count --id=10xgam_count \ --fastqs=/crex/proj/uppstore2019072/10xgams/TH-2632/200922_A00181_0206_AHT2VJDRXX/ \ --sample=SI-GA-B1_1,SI-GA-B1_2,SI-GA-B1_3,SI-GA-B1_4,SI-GA-C1_1,SI-GA-C1_2,SI-GA-C1_3,SI-GA-C1_4 --transcriptome=/crex/proj/uppstore2019072/10xgams/TH-2632/Sanger-data/Plasmodium_falciparum.ASM276v2_MM \ --expect-cells=1000 \ --localcores=26 \ --localmem=500

ERROR

For more information try --help /var/spool/slurmd/job18829903/slurm_script: line 21: --transcriptome=/crex/proj/uppstore2019072/10xgams/TH-2632/Sanger-data/Plasmodium_falciparum.ASM276v2_MM: No such file or directory

evolvedmicrobe commented 3 years ago

Hi, please reach out to support@10xgenomics.com for additional help on this, at first glance I'd be curious if there were any symlinks in the path name.