csfasta malformed qualities
2
1
Entering edit mode
10.4 years ago

Hi there,

I'm new with using color space files and I kindly need your help.

I used this tool.

to trim the csfasta files and .qual files and then used bfast scripts to create csfastq files but when I checked the csfastq I noticed that the length of quality line is not the same as the length of the color space read line, here is an example from the file:

@<@@@8=>/@@@>;>/=*/86/<.-->6/@@@@@@@@>@@@@@@@@@?@@@=@!@@@@!@@;=!@@?@!@@@@!@
@7_67_1710
T33113303330300300300201222102211011230003313330333212223121123
+
@@@@@/@@@@@@8=@6@--2.@->@-@*=@2@*2?/@=/@?8*/=.@6;@2@/<@@@*=@.@=!@@?@!@@@@!@
@7_93_1895
T000022333230021113220300000211102200002201012300032112020132202201311201
+
@@@/@<=;@@@@@6@@@@@-@628*:@@@/<@@@;@@/@6@@6@/?@/@88@;@:?@8@/6@8@/@/@<0@@@!@

Is this normal or did something wrong happen in the trimming tool?

Note: I'm using bfast script (solid2fastq) to convert the csfasta and qual files to csfastq.

Thanks in advance.

HS

trimming csfasta solid quality csfastq • 2.8k views
ADD COMMENT
0
Entering edit mode

When you used solid2fastq, are you sure you used both trimmed files and not the trimmed csfasta and the untrimmed qual?

ADD REPLY
0
Entering edit mode

Yes. I'm sure i used both trimmed csfasta and trimmed qual files.

ADD REPLY
0
Entering edit mode

I have used both of these tools (Brent's script and Neil's solid2fastq) many times and never found any problem. Just try doing it again for a small file and see if the problem persist. Also, can you figure out which step is creating the discrepancy. Is it the trimming program or the conversion program.

ADD REPLY
0
Entering edit mode

Thanks for your reply.

These are the commands I'm using, can you tell me if you notice anything wrong with them:

  1. trim the qualities < 30

    python solid-trimmer.py -c AGERI5500XL_Library1_F3.csfasta -q AGERI5500XL_Library1_F3_QV.qual -p lib1_trimmed --min-qual 30
    
  2. convert csfasta to csfastq

    ./solid2fastq lib3_trimmed_F3.csfasta lib1_trimmed_F3_QV.qual -o lib1
    

thanks.

ADD REPLY
1
Entering edit mode

Shouldn't csfasta and qual files have the same prefix? Your csfasta is lib3 and qual is named as lib1. I'm referring to the solid2fastq command.

ADD REPLY
0
Entering edit mode

They have the same prefix. I must have copied a wrong command when I wrote the post.

The command is like this:

./solid2fastq lib1_trimmed_F3.csfasta lib1_trimmed_F3_QV.qual -o lib1
ADD REPLY
0
Entering edit mode
10.4 years ago
brentp 24k

It has been a while since I used that script, but make sure you are using the one from here: https://github.com/brentp/bio-playground/blob/master/solidstuff/solid-trimmer.py

Then, you should just use it as:

python solid-trimmer.py -c AGERI5500XL_Library1_F3.csfasta \
                        -q AGERI5500XL_Library1_F3_QV.qual \
                        -p lib1_trimmed.fastq --min-qual 30

Then you won't need to use solid2fastq and you'll have a trimmed fastq (lib1_trimmed.fastq) that's ready for consumption by BFAST.

ADD COMMENT

Login before adding your answer.

Traffic: 1436 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6