Hello all,
I have now spent some time reformatting my .csfasta and .qual files to make them compatible to the new TopHat v 1.1.
I would be interested to see your approaches!
First I used the tools supplied with MAQ (fq_all2std.pl csfa2std and solid2fastq.pl). However these did not work, since they converted my colorspace code to nucleotide code.
Then I chose to use solid2fastq.c from the BFAST package and this seems to work.
I also converted the "." characters in my .csfasta to "N"s using:
and changed the negative values in the .qual file of -1 to 1:
The result looks like this:
Even though TopHat now accepts this file, I still get an error:
using
with or without the option --integer-quals.
Now I wonder if this is due to my input file or due to other problems mentioned here: http://seqanswers.com/forums/showthread.php?t=7141
What input files have worked for you and how did you generate them?
All the best,
Sebastian
I have now spent some time reformatting my .csfasta and .qual files to make them compatible to the new TopHat v 1.1.
I would be interested to see your approaches!
First I used the tools supplied with MAQ (fq_all2std.pl csfa2std and solid2fastq.pl). However these did not work, since they converted my colorspace code to nucleotide code.
Then I chose to use solid2fastq.c from the BFAST package and this seems to work.
I also converted the "." characters in my .csfasta to "N"s using:
Code:
awk '{if ( (NR-2)%4==0) {gsub(/\./,"N",$0); print $0} else { print $0}}'
Code:
sed -i 's_-1_1_g' Sample_14_Qual_minus.qual
Code:
@853_8_25 T32NN232N3N10NN123NN202NN101NN010N1120NN012N0002N0N + +*""%%%"%"%%""%%%""%)&""%%%""%%+"&'%&""'(%"'))'"&" @853_8_35 T31NN012N0N01NN011NN112NN300NNNN2N2001NN1N0N1N1NN3N + ?:""=54"@"=+""A98""745"";98""""2"=@>8""<"4"<"6"";"
Code:
[Thu Oct 7 09:32:30 2010] Beginning TopHat run (v1.1.0) ----------------------------------------------- [Thu Oct 7 09:32:30 2010] Preparing output location /home/schaefer/tophat/RBM20/Sample14/ [Thu Oct 7 09:32:30 2010] Checking for Bowtie index files [Thu Oct 7 09:32:30 2010] Checking for reference FASTA file [Thu Oct 7 09:32:30 2010] Checking for Bowtie Bowtie version: 0.12.3.0 [Thu Oct 7 09:32:30 2010] Checking for Samtools Samtools version: 0.1.8.0 [Thu Oct 7 09:32:37 2010] Checking reads min read length: 50bp, max read length: 50bp format: fastq quality scale: phred33 (default) [FAILED] Error: could not execute prep_reads
Code:
/usr/local/tophat_1.1.0/tophat --integer-quals -o /home/schaefer/tophat/Sample14 -C rn4_c /home/schaefer/tophat/fastq/Sample14Ns.fastq
Now I wonder if this is due to my input file or due to other problems mentioned here: http://seqanswers.com/forums/showthread.php?t=7141
What input files have worked for you and how did you generate them?
All the best,
Sebastian
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