Sorting barcoded Illumina data?

[xincognitax]

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[Heisman]

There is probably a better way but here are a couple of commands you will probably find useful and can play with to accomplish your goal. This will take the barcode from the header and put it at the end of the read, thus allowing you to analyze as you normally would. I'm not much of a computer person either but I had to google around a little while ago to figure this type of thing out for a different purpose.

sed -n '1,${p;n;}' [file] > odd_lines
sed -n '2,${p;n;}' [file] > even_lines

The odd_lines file will have the headers and the even_lines file will have the reads. Then, cut the odd_lines file to abstract the barcode.

cut -f2 -d # odd_lines > part_1
cut -f1 -d / part_1 > barcodes

Then paste the barcodes to the ends of the reads and get rid of the tabs that will be between them:

paste even_lines barcodes | tr -d '\011' > reads_with_barcodes

Then put the header part lines together without the barcodes:

cut -f1 -d # odd_lines > first_head
cut -f2 -d / odd_lines > second head

paste first_head second_head | tr '\t' '#/' > headers_without_barcodes

and then finally put the two files back together:

paste headers_without_barcodes reads_with_barcodes | tr '\t' '\n' > new_file_to_analyze

This should work, although there may be typos.

[xincognitax]

old delete