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Running TRUST4 with non-10X single-cell data, barcodes are in the RG:Z headers of fastq

Open LukaP-BB opened this issue 8 months ago • 6 comments

I have fastq files for scDNA with barcodes extracted in the headers, in the RG:Z field.

@A01789:135:HLKCJDMXY:1:1101:1027:1047 RG:Z:CGTGCCTATTCGGACAGT
TTAAATTGGTATCAGAAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATCCGGAAACAGGGGTCCCATCAAGGTTCAGTGGAA
+
FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF:FFFFFFFFFF:,FFFFF:FFFFFFF,F

Is there a way to use this information in a similar fashion as specifying the field when the input is a bam file ? I couldn't find it.

If there is no way to do it currently, what would be your recommended way to specify barcodes ?

I tried extracting the raw barcodes from the headers in a text file, but it seems it isn't the right solution

LukaP-BB avatar May 31 '24 14:05 LukaP-BB