fastx_collapser: found invalid nucleotide sequence

[Palgrave]

Anyone know what the reason is?

fastx_collapser: found invalid nucleotide sequence (TCTTAACCCGGACCAGAAACTA ) on line 2




>1-1460323
TCTTAACCCGGACCAGAAACTA
>2-1321361
AGGTTCCGGATAAGTAAGAGCC
>5-342436
TAGCATATCGAGCCTGAGAACA
>6-267424
TGATACGGATGTTATACGCAGC
>7-221604
CGGTTCCGGATAAGTAAGAGCC

[GenoMax]

Not answering your question but wanted to suggest that you may want to try clumpify.sh from BBMap for this purpose (http://seqanswers.com/forums/showpos...3&postcount=29). See full thread for additional information.

[gringer]

It could be the space at the end of the line. I notice that there is no space after the opening bracket, and one space before the closing bracket.

[Palgrave]

I think so. Any idea how to remove it?

[GenoMax]

sed 's/\ $//g' your_file > new_file

should do it.

[Palgrave]

Thanks. It worked