Trinity: Combining PE and SE strand-specific reads?

[oligo]

I would like to use trinity to assemble the transcriptome of a non-model eukaryote.

I have:
1. 100M: single-end, strand specific, 40bp reads.
2. 15M: paired-end, strand-specific, 75bpx2 reads.

I would like to use trinity to assemble all of the reads but could not find a way to combine SE and PE libs that are strand-specific.

Is there a way to do that, or are there other suggestions (eg different assembler)?
Merging the PE reads would probably not make a big difference.

[westerman]

Trinity will either accept pairs or singles but not both. The usual suggestion is to add the single-end reads to the end of one of the paired-end files but I am not sure if this will work with different length reads. Sending email to the users' list:

https://sourceforge.net/mailarchive/forum.php?forum_name=trinityrnaseq-users

Will get you a quick response.

[yueluo]

http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_mult_seq_libraries

[oligo]

Thank you. I was considering this (from the Trinity page):

f you have both paired and unpaired data, and the data are NOT strand-specific, you can combine the unpaired data with the left reads of the paired fragments.

...Will try

[yueluo]

Since both your PE and SE data are strand-specific:

If you have additional singletons, add them to the .fq file that they correspond to based on the sequencing method used (if they’re equivalent to the left.fq entries, add them there, etc).

Just make sure you get the orientation correct

[westerman]

Quoting myself here ... but I am not sure if this will work with different length reads.

Now that I come back to this message the answer is, "of course different length reads are allowed". I do this all of the time with trimmed reads of various lengths. Don't know what I was thinking!

The other answers to this post are all good.

[oligo]

Thank you for the suggestions. It worked.