how many bp of barcode and UMI
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0
Entering edit mode
15 months ago
yueli7 ▴ 210

Hello,

I have data: SRR3196086_1.fastq, SRR3196086_2.fastq.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133466

Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired-end mode (R1: 26 cycles; I1: 8 cycles; R2: 57 cycles)

How many bp of barcode and UMI in SRR3196086_1.fastq? The length of it is 28bp, how many bp is barcode, and how many bp is UMI?

Thanks in advance for great help!

Best,

Yue

li@Desktop-590-p0xxx:~/celseq2-master$head -n 12 SRR9609653_1.fastq @SRR9609653.1 1 length=28 GAAGANTAGAGCTTTCTTTGTATTGGTT +SRR9609653.1 1 length=28 AAAAA#EEEEEEAEEEEEEEEEEEEEEE @SRR9609653.2 2 length=28 AATCANGAGGAGCAAACCGCGGTTCAGT +SRR9609653.2 2 length=28 AAAAA#EEEEEEEEEEEEEEEEEEEEEE @SRR9609653.3 3 length=28 GTCTTNACAAAGCTCTCCTGTTTTCTTG +SRR9609653.3 3 length=28 /AAA6#A/EEEEEEEEA<E/EEEAAE/E li@Desktop-590-p0xxx:~/celseq2-master$ head -n 12 SRR9609653_2.fastq
@SRR9609653.1 1 length=56
CAGAGACTTCGTTTAGCCAAAATTGTGTAGTTTGTGAAAGTGTACAAAAAATCTGN
+SRR9609653.1 1 length=56
AA//AEEEEE/EAA<EEAEE/<E</EA<A/AE<EEEA/AEEEE/6<A<///EEEE#
@SRR9609653.2 2 length=56
ATCTACGAGGCCTGCTTTCTTCTGAATGAGGATTTGGTTTTCCATCGCCTGGTTCN
+SRR9609653.2 2 length=56
AAAAAEEAEA<EAEEE/AEAEEEEEEEA/EEEE<E//EEEE6AEEA/E<E</AA<#
@SRR9609653.3 3 length=56
TATCATTACAGTTTGACTCTGTATAGTCACTACACTCGTTAGCATTGCTGAGTAAN
+SRR9609653.3 3 length=56
AAAA/A/E6E/</A///<EAAA//EE/6<EAEA/6A//EA/E</<//6/<AEEA6#

RNA-Seq • 330 views
3
Entering edit mode
15 months ago
GenoMax 102k
16 bp cell barcodes + 10 bp UMI (V2 chemistry)
16 bp cell barcodes + 12 bp UMI (V3 chemistry)


Looks like you have V3 data.

0
Entering edit mode

Hello, genomax,

Thank you so much for your responding!

Thank you again!

Best,

Yue