csfasta malformed qualities

Question

[Hatem Elshazly]

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

[Devon Ryan]

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

[Hatem Elshazly]

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

[Ashutosh Pandey]

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.

[Hatem Elshazly]

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.

[Jordan]

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.

[Hatem Elshazly]

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

Answer 1

[brentp]

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.