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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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How to add my own barcode whitelist？ #98

Closed listen2099 closed 3 years ago

listen2099 commented 3 years ago

I am testing a dataset with follow Fastq header and Reads structure, but cellranger count complains "an extremely low rate of correct barcodes was observed for this chemistry", It seems that cellranger do not support my data, how can I add DEFINED library information in cellranger count?

Index: 8 bp Read1: 30 bp = 20 barcode + 10 UMI Read2: 90 bp

x108_S1_L001_I1_001.fastq.gz @MGISEQ:1:DP8400011054TL:1:731589:57:53 1:N:0:AGGTTGGG AGGTTGGG + FFFFFFFF @MGISEQ:1:DP8400011054TL:1:533701:57:49 1:N:0:AGCATCCA AGCATCCA + FFFFFFFF @MGISEQ:1:DP8400011054TL:1:731626:57:53 1:N:0:CTGAGTAT CTGAGTAT

x108_S1_L001_R1_001.fastq.gz @MGISEQ:1:DP8400011054TL:1:731589:57:53 1:N:0:AGGTTGGG GCCTGTGCGTTACGAAGTGCAGGCATTTGC + DDDEE?EEDD?GHEFE>@DFDF;6F/FFE8 @MGISEQ:1:DP8400011054TL:1:533701:57:49 1:N:0:AGCATCCA GTGAGCGGAAATGTCCGTGCATGCAGATGT + FAEEFEFA9CDFEHFFFAEEGF@CEEBHEC @MGISEQ:1:DP8400011054TL:1:731626:57:53 1:N:0:CTGAGTAT GTGTCGCGGAAGCAAGCGACTACGTCACGT

x108_S1_L001_R2_001.fastq.gz @MGISEQ:1:DP8400011054TL:1:731589:57:53 2:N:0:AGGTTGGG CTGTGGGACCTGTGTGCTGGGCAAGGGAGTCTGTCCATCTGCCTGTGTTCGCATACCTAGACTTTTCCAGGGTTTCCAGAAACAGAGAAA + DFFDFDDEFEEDAGDFEEEDEFFEE?BEEEDECDDEFFFFGEFDEEGEEFCEFEEEEGGADEGD3EDEEGEEDCEBEGEFFEEHDEEEGE @MGISEQ:1:DP8400011054TL:1:533701:57:49 2:N:0:AGCATCCA GTCTCTATCTAAAAAATATAAGGGGCTGGAGATACAGGTCAGAGGTTAAGAACATACATTGTGCTTTCAGAGAACTCAAGTACTATTCCT + CADGEEFEEGEDFCEBFFEEFDEDEFDDC8B:EFEF>CDFFDBEEDEDDE5FDDFFDEFFD9EFFFEEGDDE)EFEFGDECFDFG2E<FF @MGISEQ:1:DP8400011054TL:1:731626:57:53 2:N:0:CTGAGTAT TATATGTTTCTCTGAACCTGACCTCCCTCTACAACAGTATCTTTCTAGTTGAGTACTAGGATTTAAAACAAACAAACAAACAAGGCCCCA

evolvedmicrobe commented 3 years ago

The Cell Ranger software (as discussed in the license) does not support non-10X generate data except under some conditions. Email support@10xgenomics.com for more help and information.

chentingwei908 commented 3 years ago

Hello, I recently encountered a similar problem with you. The result of CellRanger seems to show that the comparison rate of barcode is too low. We use the single-cell reference genome of rhesus monkey established by ourselves. I'd like to know if you have solved this problem. I'm looking forward to your reply. Thank you