Barcode 'AAACCCATCTCCCAAT-1' has wrong length and WARNING: Can't find chromosome 'JH584301.1'

[BeyondMyPast228]

Hi, Thanks for developing this amazing tool. I used this software for the first time. But when I processed the Cellranger's output BAM file with dropEst, the following error occurred.(My code is: ~/dropEst/dropest -m -f -F -L eiEIBA -o run1 -g /data/singlecell/refdata-cellranger-mm10-3.0.0+td+GFP/genes/genes.gtf -c ~/dropEst/configs/10x.xml /data/jr/A15762/outs/possorted_genome_bam.bam )

/data/jr/A15762/outs/possorted_genome_bam.bam: 320000000 primarily aligned reads (11.2% intergenic, 69.6% touch exon, 18% touch intron, 0.78% touch both gene and not annotated regions, can't parse 1.96595% reads, ), 0 non-mapped reads, 1222441 CBs read WARNING: Can't find chromosome 'JH584301.1' WARNING: Can't find chromosome 'GL456379.1' WARNING: Can't find chromosome 'GL456393.1' WARNING: Can't find chromosome 'GL456366.1' WARNING: Can't find chromosome 'GL456367.1' WARNING: Can't find chromosome 'GL456239.1' WARNING: Can't find chromosome 'GL456213.1' WARNING: Can't find chromosome 'GL456383.1' WARNING: Can't find chromosome 'GL456385.1' WARNING: Can't find chromosome 'GL456360.1' WARNING: Can't find chromosome 'GL456378.1' WARNING: Can't find chromosome 'GL456389.1' WARNING: Can't find chromosome 'GL456372.1' WARNING: Can't find chromosome 'GL456370.1' WARNING: Can't find chromosome 'GL456390.1' WARNING: Can't find chromosome 'GL456394.1' WARNING: Can't find chromosome 'GL456392.1' WARNING: Can't find chromosome 'GL456382.1' WARNING: Can't find chromosome 'GL456359.1' WARNING: Can't find chromosome 'GL456396.1' WARNING: Can't find chromosome 'GL456368.1' /data/jr/A15762/outs/possorted_genome_bam.bam: 326401344 primarily aligned reads (11.1% intergenic, 69.7% touch exon, 17.9% touch intron, 0.774% touch both gene and not annotated regions, can't parse 1.96674% reads, ), 0 non-mapped reads, 1236842 CBs read Bams parsed: 17:18:07.

82472 CBs with more than 20 genes top CBs: 12407 CTTACCGTCCTAACAG-1 12021 CAAGACTTCTCGGCTT-1 11623 TTATTGCTCATTGCGA-1 11199 ACGGTTATCTTAGCCC-1 11194 GGCTTGGCACGCAGTC-1 10990 CCTCTCCTCATCGCAA-1 10872 TCATATCAGCATCGAG-1 10508 GGCAGTCCATACCATG-1 10495 ATCAGGTAGCTGAAAT-1

Start merge: 17:18:29. Merge initialized: 17:18:29. Barcode 'AAACCCATCTCCCAAT-1' has wrong length (16 expected)

In addition, I wonder if the output result of dropEst is also a file in BAM format. How can I solve this problem? I sincerely hope you can help me.

[evanbiederstedt]

What protocol are you using?

[TANDAMAO]

Hi! Have you solved this problem? I have exactly the same issue (Barcode 'AAACCCATCTCCCAAT-1' has wrong length (16 expected)). My data was produced by 10x 5'scRNAseq. I have tried to modify the barcode length in 10x.xml but nothing changes.

[LikaiTan]

: **~/dropEst/dropest -m -f -F -L **

Hi, I think if you drop the -m in your code problem will be solved.