How to set the correct preset for my data

[pandahui01]

This is my align.txt

Analysis time: 31.56s
Total sequencing reads: 9035215
Successfully aligned reads: 529014 (5.86%)
Coverage (percent of successfully aligned):
CDR3: 431900 (81.64%)
FR3_TO_FR4: 405582 (76.67%)
CDR2_TO_FR4: 404692 (76.5%)
FR2_TO_FR4: 394254 (74.53%)
CDR1_TO_FR4: 393549 (74.39%)
VDJRegion: 412315 (77.94%)
Alignment failed: no hits (not TCR/IG?): 6828336 (75.57%)
Alignment failed: absence of V hits: 5955 (0.07%)
Alignment failed: absence of J hits: 1671910 (18.5%)

I looked at the previous preset discussion and used 10x-bulk.yaml because my data came with umi, and did breaks to allow it to be assembled into a full-length sequence (PE150)

Can you help me? Thank you!

[mizraelson]

Hi, yes the 10x-bulk.yaml preset should work, but you will have to specify the pattern manually that describes you UMI structure.

[pandahui01]

The format of my.fq files is as follows:
read1.fq: 25bp (barcode)+10bp(umi)
read2.fq: 150bp (vdj)
I'm facing an issue where I'm unsure how to accurately specify/define my multiple barcode sequences as a single cell for analysis. I've made an attempt using 10x-bulk.yaml, considering 35bp as umi, and up are the results I got.
So I used 10x.yaml .I generated the whitelist myself, but get error
can you help me to set the suitable preset for me?

[mizraelson]

I am not sure I understand. Is it a single cell data or not? In R1: 25bp (barcode)+10bp(umi) what is the 25bp barcode?

[pandahui01]

I am sorry for my late reply. It is stereo-seq data. the 25bp barcode is like a dnb code, One cell covers many dnbs.  熊喵 ***@***.***  

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