ERROR_00201: unknown file format: the read ID should start with @ or >

[Pepinos]

Hello,

I'm having trouble aligning the test files above. At first I thought the problem came from multiline fastq files but then I converted them to single-line files and keep getting the same error. The minimal test case above produces the error. Am I missing something obvious?

Thanks,
Petros

[Alexander Dobin]

Hi Petros,

gzip -c compresses the file, but you need to uncompress them, i.e.

--readFilesCommand gunzip -c 

OR, if it's installed on your system,

--readFilesCommand zcat

Cheers

Alex

[kenny...@gmail.com]

can u tell me  how to convert multiline fastq files  to single-line files ?

在 2014年12月22日星期一 UTC+8上午6:48:37，Pepinos写道：

[Alexander Dobin]

Hi @kennyzhao94

assuming that your quality scores (and sequences) do not contain @ or + characters, you need to check for strings

that start with "@" : this would be the read ID, and "+" : this would be the line separating sequence lines(s) from the quality scores line(s).

Cheers

Alex