The C binary from bfast
solid2fastq 0.6.4a
Usage: solid2fastq [options]
-c produce no output.
-n INT number of reads per file.
-o STRING output prefix.
-j input files are bzip2 compressed.
-z input files are gzip compressed.
-J output files are bzip2 compressed.
-Z output files are gzip compressed.
-t INT trim INT bases from the 3' end of the reads.
-h print this help message.
send bugs to bfast-help@lists
solid2fastq.pl from bfast-0.6.4a
with notes in the script to refer to the above
# Author: Nils Homer
# Please see the C implementation of this script.
EDIT: THANKS to iceman for his reminder in the comments
"Make sure that you use the BWA's solid2fastq.pl if you are going to use BWA as it "double-encodes" the reads."
solid2fastq.pl from bwa-0.5.7
Usage: solid2fastq.pl
Note:
".csfasta" read file. Then
file and
paired; otherwise reads will be regarded as single-end.
The read name will be
tag and `2' for F3. Usually you may want to use short
to save diskspace. Long
# Author: lh3
# Note: Ideally, this script should be written in C. It is a bit slow at present.
# Also note that this script is different from the one contained in MAQ.
maq-0.7.1/scripts/solid2fastq.pl
Usage: solid2fastq.pl
Note:
".csfasta" read file. Then
file and
paired; otherwise reads will be regarded as single-end.
The read name will be
tag and `2' for R3. Usually you may want to use short
to save diskspace. Long
# Author: lh3
# Note: Ideally, this script should be written in C. It is a bit slow at present.
Use the BFAST C-version for speed, but the perl version is easier to customize. Make sure that you use the BWA's solid2fastq.pl if you are going to use BWA as it "double-encodes" the reads.
ReplyDeleteThe lastest version of the solid2fastq program in the bfast+bwa branch of bfast includes a few additional options. Some relevant ones:
ReplyDelete-b encodes the output in the format bwa wants (double encoded, reads order reversed)
-w leaves the output in color space, but splits the reads in into read1, read2, and single files.
There's also a psolid2fastq.pl script, which will convert and split the files in parallel on an SGE cluster. It works surprisingly well if splitting reads is useful for you. (Disclaimer: I wrote the script.)
Hey,
ReplyDeleteI am using MAQ for the first time. I attempted to use solid2fastq.pl and it executes without any errors, however, the files it produces are empty.
I have PE reades "_F3.csfata" and "_R3.csfasta" with their corresponding Qual files.
I have no clue why this is happening. Any ideas??
Hi Anonymous, I would advise you to try to use BWA if you can.
ReplyDeleteperhaps you can paste your entire command with solid2fastq.pl?
with the names of your files?
Hi I have bwa-0.5.9/solid2fastq.pl version. I have two files SolF3.csfasta & SolF3_QV.qual which i want to convert in 'fastq'. After running the command as :
ReplyDeleteperl /usr/local/ngs/bwa/bwa-0.5.9/solid2fastq.pl Sol SolTest
I am getting the file SolTest.single.fastq.gz but with no reads in file after i unzip it, whereas i have good and equivalent amount of reads in my input file.Can you explain me the reason if you have any idea.
Strange to say the say command is working with another set of file....
You can reply me on my mail id brajbio.22@gmail.com
@braj sounds like a problem I had before .. did you delete the comments header in the csfasta and qual file? I vaguely recall those gave me problems with some scripts.
ReplyDeletei want to convert csfasta file to .fastq format so please help
ReplyDeletethanking
vijay sharma
The first script is correct in its R3 / F3 conversion to 1 / 2 .
ReplyDelete" The read name will be :panel_x_y/[12] with `1' for R3 tag and `2' for F3. "
The second is incorrect in that it names F3 as 1 and R3 as 2.