|Thread||Thread Starter||Forum||Replies||Last Post|
|Unmatched read name error when converting csfasta to fastq with solid2fastq.pl||yksikaksi||Bioinformatics||2||11-06-2011 09:18 PM|
|Problem converting solid2fastq with Barcode||m_elena_bioinfo||Bioinformatics||7||09-15-2011 08:17 AM|
|Has somebody noticed that BWA' little scirpt solid2fastq.pl has some fatal defeat?||ryuky||Bioinformatics||3||04-23-2011 07:26 PM|
|solid2fastq paired-end||m_elena_bioinfo||Bioinformatics||2||07-08-2010 09:11 AM|
|05-25-2010, 05:20 AM||#1|
Join Date: May 2010
I just got a question. I wanna align SOLID data with BWA and therefore transformed it in FASTQ files with the solid2fastaq.pl script. But the script does not take the whole sequence of the csfasta but excludes the first two bp. In my opinion it would make sense to exclude the first base, as it is not in color space but not two.
Here an example:
an entry of my csfasta files has following sequence
and the output in the FASTQ file is a sequence with:
By comparing the sequences it can be seen that two bp are missing:
this is because of line 100 in the script delivered by BWA 0.5.7 in the method read1:
$_ = substr(<$fhs>, 2);
This funktions takes the sequence beginning from the 3rd position.
Is there any reason for this or is this an error ?
Thanks for answering
|05-25-2010, 09:04 AM||#2|
Location: Boston, MA, USA
Join Date: Nov 2008
The first color encodes the adapter and the first base, and therefore is partly dependent on DNA not present in the underlying genome (the adapter). BWA trims the first color and adapter so you lose the first two bases (a 50bp reads is now 48bp). This is performed so when the color read is compared to the encoded reference (in color space), the colors from the read will match the color reference exactly (when there is no error). Including the first color (or adapter) would violate those rules. Nonetheless, you lose two bases from each read, which BWA should be able to include/recover during local alignment (Smith-Waterman/Needleman-Wunsch), but does not. Other software, like BFAST (I am the author), can use all the bases in the final alignment, so it is possible. You should bug the BWA author (lh3) to remove the 2bp base trimming as it is not going to be fixed by changing the solid2fastq.pl, but only through changing much of the BWA color space code.
It also seems like SOLiD support is an afterthought of many alignment software authors. Such a shame, since it is a much more fun and challenging problem to try and properly align in color space.
|05-26-2010, 12:58 AM||#3|
Join Date: Nov 2009