Extract barcodes (sample and UMI) from read names

[nh13]

In some cases, we get FASTQs that have sample barcodes and UMIs in the read name and I we'd like to extract those. Is that possible?

See:
[1] https://help.basespace.illumina.com/files-used-by-basespace/fastq-files
[2] https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002211

[Yenaled]

This feature is not available yet. I'm working on some major upgrades to splitcode this month, and I'll be sure to add this in in the next week or two.

[Yenaled]

@nh13 Sorry, am very late haha, but I finally got around to adding the feature (along with many other features) to the newest version of splitcode:

https://splitcode.readthedocs.io/en/latest/extracting_from_names.html

Test it a bit and it seems to work.

Still updating the documentation a bit.

[clintval]

I tried this but couldn't get it to work for my use case.

I have conventional FASTQ files from Illumina in which the UMI and sample index(es) are in the read name and comment:

@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos>:<UMI> <read>:<is filtered>:<control number>:<index>

I am trying to extract the UMI (8th-field of name) and sample ID (4th-field of comment) to RX and BC SAM tags.

Importantly, the UMI can be - delimited.

An example would be:

@A01000:460:XXXXXX:1:2101:10004:10081:ACGT-TTTT 1:N:ATCCC+ATCG
GGGGAGAGAGCGATAGACATA
+
JJJJJJJJJJJJJJJJJJJJJ

Where ACGT-TTTT is the UMI and ATCCC+ATCG are the sample indexes.

When I try to extract this information with splitcode, I get only the sample indexes re-appended back to the read:

$ splitcode \
     --out-bam \
     --pipe \
     --from-name '0,0,0,::;0,0,0,::+' \
     "test.fastq" \
     | samtools view
A01000:460:XXXXXX:1:2101:10004:10081:ACGT-TTTT 1:N:ATCCC+ATCG	12	*	0	0	*	*	0	0	ATCCCATCGGGGGAGAGAGCGATAGACATA	KKKKKKKKKJJJJJJJJJJJJJJJJJJJJJ

If I then try to "re-extract" using extract syntax, I oddly extract into the original read as if the sample indexes are being prepended after any extractions occur.

 splitcode \
     --out-bam \
     --pipe \
     --from-name '0,0,0,::;0,0,0,::+' \
     --extract '0:0<umi1[9]>' \
     --x-names \
     "test.fastq" \
     | samtools view
A01000:460:XXXXXX:1:2101:10004:10081:ACGT-TTTT 1:N:ATCCC+ATCG	12	*	0	0	*	*	0	0	ATCCCATCGGGGGAGAGAGCGATAGACATA	KKKKKKKKKJJJJJJJJJJJJJJJJJJJJJ	RX:Z:GGGGAGAGA