Problem to align colorspace data in bowtie1

Question

[gufernandez10]

Hi I download a data set from SRA database get from ABI Solid 4 System platform, I used the following command:

bowtie ../../Syne -C -S -p 7 --best --strata -m 1 ../stdc_1.fastq >stc_1.sam

to get uniquely mapped, but after a minutes running the alignment abort showing:

Reads file contained a pattern with more than 1024 quality values.
Please truncate reads and quality values and and re-run Bowtie
terminate called after throwing an instance of 'int'
Abortado

Reading in forum they say that its a problem with multiples "." in a group of read, to solve that I removed that group of read and the problem persist.

Any idea of why is happening or if I'm doing something wrong?

Thanks

Answer 1

[Antonio R. Franco]

Run a Fastqc analysis of the reads. I believe your sequences are not that long and you will have to trim them

Answer 2

[gufernandez10]

thank for answer.

I tryed run fastqc but I believe that my file is to big because just charge the 35% of the file and keep stoped and I don't know a tool better than fastqc to take a look to colorspace file. I dont think that the problem its the hardware because is a server over 30GB of ram. I just see the Ns as a probably target of trimm and were removed but problem persist.

Answer 3

[Antonio R. Franco]

You always get "N" (read ".") when using SOLiD..

[gufernandez10]

do you know some tool that make a good transformation of solid data to illumina data?

[Antonio R. Franco]

You cannot and must not convert colospace sequences to Illumina sequences (ATGC). The reason can be found if you google a little bit

In my hands, I had a lot of trouble handling SOLiD data. A mapping to a nice transcriptomic using bowtie did not render more than 5-7% of the reads being mapped, and after a lot or work, I eventually give up..

Answer 4

[xiaoshen19930901]

i suggest the following codes This edition of software is important !!!! export PATH="/usr/local/src/tophat-1.4.1.Linux_x86_64/:$PATH" export PATH="/usr/local/src/bowtie-1.0.1/:$PATH"
export PATH="/usr/local/src/samtools-0.1.18/:$PATH"

cd /home/sjshen/project/GaoSR_PGC_RNA/2.Persistent/0.2_fastq_cut/convert/fastaqual species=mm10 thread=10

for i in *.fna do echo $i t=${i/.fna/.qual} echo $t (nohup tophat -p $thread -G $GTF_dir/${species}.gtf --color --quals --no-coverage-search \ -o $tophat2_dir/${i%%.fna}.tophat2_out /home/sjshen/project/GaoSR_PGC_RNA/2.Persistent/bowtie_index_color/${species} $i $t > $tophat2_dir/${i%%.fna}.tophat2.log) & done

echo $tophat2_dir cd $tophat2_dir

finish