trimmomatic

[Safoora Amin]

Dear Brian

I have a sample with 5 replicate and I try to trim by trimmomaticversion 0.32. I try the following command line and got this message :

java -jar /bioapps/Trimmomatic-0.32/trimmomatic-0.32.jar PE -basein RC-BS1a-6_CCGTCC_L003_R1_001.fastq.gz RC-BS1a-6_CCGTCC_L003_R2_001.fastq.gz -baseout RC-BS1a-6_CCGTCC_L002_R1_p001.fastq.gz RC-BS1a-6_CCGTCC_L002_R1_u001.fastq.gz RC-BS1a-6_CCGTCC_L002_R2_p001.fastq.gz RC-BS1a-6_CCGTCC_L002_R2_u001.fastq.gz

and I got this , this is not error but message 

TrimmomaticPE: Started with arguments: -basein RC-BS1a-6_CCGTCC_L003_R1_001.fastq.gz RC-BS1a-6_CCGTCC_L003_R2_001.fastq.gz -baseout RC-BS1a-6_CCGTCC_L002_R1_p001.fastq.gz RC-BS1a-6_CCGTCC_L002_R1_u001.fastq.gz RC-BS1a-6_CCGTCC_L002_R2_p001.fastq.gz RC-BS1a-6_CCGTCC_L002_R2_u001.fastq.gz

Multiple cores found: Using 16 threads

Using templated Input files: RC-BS1a-6_CCGTCC_L003_R1_001.fastq.gz RC-BS1a-6_CCGTCC_L003_R2_001.fastq.gz

Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: RC-BS1a-6_CCGTCC_L002_R2_p001.fastq.gz

        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:60)

        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:495)

        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)

could you please tell me what am i doing wrong?

Regards

[Brian Haas]

Hi Safoora,

You can check with the trimmomatic developers regarding these issues.

If you want to run it within trinity, just use the Trinity --trimmomatic parameter.

If you want to use a different version if trimmomatic than what comes bundled with trinity, you can probably just drop in the new jar file as a replacement in the trinity plugins area.

Best,

-Brian

(by iPhone)

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[Brian Haas]

Try

   Trinity --trimmomatic --left RC-BS1a-6_CCGTCC_L003_R1_001.fastq --right

RC-BS1a-6_CCGTCC_L003_R2_001.fastq  --max_memory 100G --CPU 10  --seqType fq

and adjust parameters as needed.

If you want to set the trimmomatic params to custom values, that should be possible, but see the usage info for the syntax

best,

~b

On Wed, Mar 4, 2015 at 10:32 AM, Safoora Amin <minami...@gmail.com> wrote:

Dear Brian

 I use Trinity , and the sample names are:

RC-BS1a-6_CCGTCC_L003_R1_001.fastq

RC-BS1a-6_CCGTCC_L003_R2_001.fastq

I run following command :

Trinity --trimmomatic --quality_trimming_params right RC-BS1a-6_CCGTCC_L003_R1_001.fastq

but I got this error:

Error, do not understand options: RC-BS1a-6_CCGTCC_L003_R1_001.fastq

Can you help me do it?

Sorry I do not have any one helping me.

Thank you

Regards

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Brian Haas]

Right. It does trimming followed by assembly, and should only be using the paired/trimmed (P) set for it.

You should be able to have one Trinity command that does it all, including your replicates.  Use commas to separate the replicates like so:

     --left  repA_r1.fq.gz,repB_r1.fq.gz  --right  repA_r2.fq.gz,repB_r2.fq.gz

along with your other parameters.

best,

~brian

On Wed, Mar 4, 2015 at 8:10 PM, Safoora Amin <minami...@gmail.com> wrote:

Dear Brian

After finishing the trimming , I have several file including :

L003_R1_001.fastq.P.qtrim.gz

L003_R1_001.fastq.PwU.qtrim.fq

L003_R1_001.fastq.U.qtrim.gz

L003_R2_001.fastq.P.qtrim.gz

L003_R2_001.fastq.PwU.qtrim.fq

L003_R2_001.fastq.U.qtrim.gz

Trinity.fasta

P is paired sequence, U is unpaired , and PwU means paired with unpaired?

And Trinity.fasta is the assembled file? it means that It did trimming and assemble together? with one command line?

Now for the generation of reference transcriptome (Merged assembly) , I have 2 replicate for each sample so first

gunzip   L003_R1_001.fastq.P.qtrim.gz 

then cat  2 right and 2 left to gether :

cat L003_R1_001.fastq.P.qtrim.gz  L004_R1_001.fastq.P.qtrim.gz >  righ _R1_001.fastq.P.qtrim.gz

then again cat all right of all sample and all left , and then run the 

Trinity --seqType fq --left ref_left.fq --right ref_right .fq --CPU 10 --max_memory 100G

Thank you in advance.

Regards

 

On Thu, Mar 5, 2015 at 12:05 AM, Brian Haas <bh...@broadinstitute.org> wrote:

sure thing.  best of luck!

~b

On Wed, Mar 4, 2015 at 11:04 AM, Safoora Amin <minami...@gmail.com> wrote:

Thank you so much.

Regards