Question: gmapper and colorspace
0
gravatar for jannetta.steyn
3.4 years ago by
United Kingdom
jannetta.steyn0 wrote:

Hi Folks

I hope there is someone out there that can help me. I have been struggling to use gmapper (SHRIMP2) to do some alignment on SOLiD colorspace files.

This is the top few lines of my fastq file (First question - is this actually colorspace?):

@SRR553457.1 s0811_20110511_PE_BC_2_576_555_m1_2_1181_904/1
T201230020002222222200322.2120002003020000203202001
+
!?@**@='%(7%:'&%+8%.'&(%.!&)&,%&;(-&-9%%'(='),1(*&'
@SRR553457.2 s0811_20110511_PE_BC_2_576_555_m1_3_26_1138/1
T003.3030113003001012310310200332130313300203003202
+
!4%6!&+2%51+3+*&&7%4+&*%.&&825;&>%&3%60++5'(%6'2+*4
@SRR553457.3 s0811_20110511_PE_BC_2_576_555_m1_3_27_334/1
T00320210002002221011200032100210001200022012220022

 


This is my command line:

gmapper-cs --no-qv-check -Q -N 8 -o 5 -h 80%  SRR553457.fastq    /users/njss3/PTESFinder/data/chr1_GL383518v1_alt.fa  >SRR553457.sam 2>SRR553457.log

note: detected fastq format in input file [SRR553457.fastq]
- Processing read file [SRR553457.fastq]
done r/hr r/core-hr
There has been a problem reading in the read "SRR553457.1", the quality length exceeds the sequence length!
Are you using the right executable? gmapper-cs for color space? and gmapper-ls for letter space?

 

Kind Regards

Jannetta


This is the error I am getting in the log file:

 

alignment • 995 views
ADD COMMENTlink written 3.4 years ago by jannetta.steyn0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 761 users visited in the last hour