Barcode 'AAACCCATCTCCCAAT-1' has wrong length and WARNING: Can't find chromosome 'JH584301.1'
BeyondMyPast228 opened this issue · 3 comments
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.
What protocol are you using?
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.
: **~/dropEst/dropest -m -f -F -L **
Hi, I think if you drop the -m in your code problem will be solved.