Filtering out reads with unkown base

[harlock0083]

Dear All,

I'm using fastx toolkit to remove reads with unkown bases however I'm getting an error for "invalid nucleotide sequence".

Here's part of the fastq file

@HWI-ST261:1:1:1470:2174#CGATGT/1
TGAAACTG.G.TTT.C.................................C
+
__`__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:1:1:1408:2220#CGATGT/1
GCCAGTCA.AAGTTGAGGCAGCTTCAAAAGATGGTCCATGATATTAAAAA
+
gggggcddBdccaccfggggggggggggggYcffagggegebaggggcdg
@HWI-ST261:1:1:1449:2221#CGATGT/1
GCGACTTT.ACCGAGAGGCTGCTGGAGCTCGTGTTTGGACGCGATGTTTC
+
bbbbbbbbBb`aab^bbbbb`QQV^BBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:1:1:1385:2244#CGATGT/1
AATAATCTCTGTCTTTCAGAAGCCCCAGGTTGATCTTGAATTAAATAACA
+
dggggggggggdggggggggggggggggecceddgeeggeebgedggddg
@HWI-ST261:1:1:1648:2175#CGATGT/1
ATCTGTTT.T.TTG.C.................................T
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

I'm assumiong the a "." is an unkown base. Is there a efficient script I can use to change the "." to N's?

[Oliviervg]

I have exactly the same problem,
Can anyone help ?

Thanks

[zhidkov.ilia]

One of many options is to use Galaxy (http://main.g2.bx.psu.edu/): turn your fastq file to tabular and replace the dots with 'N' in second column, then convert the table back to fastq.
(You can look on Galaxy text manipulation tutorials)

Quick and dirty is:

sed 's/\./N/g'  OLDFastq > NewFastq

Ilia

[Oliviervg]

Thank you for your answer, but I still have some problems :

Your first proposition with Galaxy includes I have to upload my fastq files (more than 40Go for one files), so it's not possible.

The second proposition, with "sed" should work, but there also "." in the quality score, and if I change all the "." by "N", there will be some errors ?

Thank you

[zhidkov.ilia]

This was modified from Aaaron Quinlan approach:

awk 'BEGIN{srand()}; {OFS="\t";getline seqs; getline sep; getline quals; print $0,seqs,sep,quals}' OldFastq | perl -pe 's/\./N/g' $2 | awk '{OFS="\n"; print $1,$2,$3,$4}' > NewFastq

Ilia

[Oliviervg]

It seems to work !
Thank you !