Question: Problem to align colorspace data in bowtie1
0
gravatar for gufernandez10
3.5 years ago by
Chile
gufernandez1010 wrote:

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 minuts running the alingment 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 im doing somthing wrong?...

 

thanks

ADD COMMENTlink modified 24 months ago by xiaoshen199309010 • written 3.5 years ago by gufernandez1010
0
gravatar for Antonio R. Franco
3.5 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:
Run a Fastqc analysis of the reads. I believe your sequences are not that long and you will have to trim them
ADD COMMENTlink written 3.5 years ago by Antonio R. Franco4.1k
0
gravatar for gufernandez10
3.5 years ago by
Chile
gufernandez1010 wrote:

thank for answer.   

I tryed run fastqc but i belive 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.

ADD COMMENTlink written 3.5 years ago by gufernandez1010
0
gravatar for Antonio R. Franco
3.5 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

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

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Antonio R. Franco4.1k

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

ADD REPLYlink written 3.4 years ago by gufernandez1010

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..

ADD REPLYlink written 3.4 years ago by Antonio R. Franco4.1k
0
gravatar for xiaoshen19930901
24 months ago by
xiaoshen199309010 wrote:

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

ADD COMMENTlink written 24 months ago by xiaoshen199309010
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