Searching for the conserved pattern containing a barcode of various length
Hi all,
I wanna to look for a pattern in the sequence, that would contain a conservative flanks and a wildcard piece inside of variable length.
In particular, I am checking the RADseq paired end data and looking for the short loci aiming to trim off the ligation_adapter from R1 and the cut_site_1-barcode-ligation_adapter from the R2.
Such reads look like this:
R1: cut_site_1-NNNNNNNNNN-cutsite_2-ligation_adapter
R2: cut_site_2-NNNNNNNNNN-cut_site_1-barcode-ligation_adapter
The problem is with trimming of R2: there is a conserved cut_site_1 & ligation_adapter sequences, but also there are 96 different types of barcodes, which sequence can be 4-8 bp long. I think I should use the wildcard, but how to specify a wildcard with varying length at the same time?
Glib
My
• 1,724 views
•
link
updated
by
Ram
•
written
by
mazepago •
•
written
by
mazepago •
1 answer
Log in to answer this question.
More posts like this
-
How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
written by Ana •
-
Sample-level demultiplex raw FASTQ file
written by Bhavya •
-
Split Visium spatial fastq according to barcodes
written by ThaiosX195 •
-
16S amplicon sequencing input data (spreadsheet): barcode vs. linker primer seqs?
written by sovrappensiero •
-
Extract the true single-cell RNA sequencing reads for running SAHMI
written by 573704669 •
-
Sc-RNA seq 5’ V2 PE auto detected by CellRanger as R2 only chemistry
written by ashley.fletcher2 •
-
Cellranger output .bam file does Not contain barcodes ( CB and UB )
written by Gabriel
-
Tutorial: scRNA-seq CITE-seq-count bioinformatics
written by colindaven
-
How to extract sequence by flanks from Fatsq R1 read
written by doc.pombe •
-
Trim read-specific adapter in paired-end reads
written by Nicolas Rosewick
