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Problem wth using the new format Illumina

Posted by valeu on Wed 08 of July, 2009 23:18 MYT

Dear Colin,

I have data from Illumina pipeline version 1.4, but then I set " -F ILMFQ " I get
Error: File format is not compatible with -F option

without any " -F " the format is identified as Sanger FASTQ
# Interpreting input files as Sanger FASTQ.

This is an example from my file 

@HWUSI-EAS454:1:2:0:1528#0/1
TCTAGGATGTGCCTAGGCTCTCGCTACACGGCATTGTGACATATCACTGC
+HWUSI-EAS454:1:2:0:1528#0/1
aa^G[`a_]\aa[`aX]`[aWMYR]`_a_G`a_a_`WZ]WOVUW^_a[`Z
@HWUSI-EAS454:1:2:0:992#0/1
CTGCCCAGAAGGCAGCATTGCCATTTCTTGCTACTTTTTTGTCTGGTTTT
+HWUSI-EAS454:1:2:0:992#0/1
^I^ba`baa__XZaab^XV`O_WYba_bYNabXaaaSVa[HID[YJQ^b^


Thank you in advance!
Valentina

Reads: 24553

Posted by colin on Thu 09 of July, 2009 08:58 MYT

Hi Valentina,

It looks like I've got a problem there in that Novoalign is still looking at the filename and deciding the file is Sanger fastq from the name and then not allowing -F ILMFQ as an alternative. I'll revise the code and issue an update asap.

In meantime you could rename the file or create a symbolic link with a name in format *_sequence.txt

Colin

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Posted by colin on Thu 09 of July, 2009 16:02 MYT

Dear Valentina,

I just put up a new release V2.05.04 that should fix you problem Could you let me know if it fixes the problem.

Thanks, Colin

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Posted by valeu on Thu 09 of July, 2009 17:06 MYT

Hi Colin,

Thank you for your quick reply! Now it works perfectly well!

Cheers,
Valentina

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