Genome guided assembly with Trinity using STAR genome index

Question

[nikelle.petrillo]

Hi all,

I am new to STAR and new to genome guided assembly in general; I have more experience with de novo assembly.

I would like to use trinity to assemble my fastq reads against a genome assembly. Am I supposed to supply the .sam file (I guess it would be coordSorted.bam after sorting/coordinating) that was outputted after I used STAR to generate a genome index?

If yes, would I be using the Trinity parameter --genome_guided_bam ?

Thanks for the help! Nikelle

[st.ph.n]

You can provide the BAM file. I'm not sure if Trinity will complain if it is in SAM format. See here for tutorial. Make sure you sort you BAM/SAM file with samtools sort

Ex.

 Trinity --genome_guided_bam rnaseq.coordSorted.bam \
         --genome_guided_max_intron 10000 \
         --max_memory 10G --CPU 10

[nikelle.petrillo]

Thanks @st.ph.n, So, is it okay to use the genome index i generated from STAR in my genome guided trinity command?

[st.ph.n]

Yes, the sorted bam file. Snippet from the tutorial page, referenced above:

Users must provide read alignments to Trinity as a coordinate-sorted bam file. Use GSNAP, TopHat, STAR or other favorite RNA-Seq read alignment tool to generate the bam file, and be sure it's coordinate sorted by running 'samtools sort' on it.

[Chanderkant Chaudhary]

Greetings,

I am also new to this. I wants to use genome guided function of trinity and I am confused that which file to use as sorted.bam. I have generated bam & Sam files via STAR. I guess bam sorted file is the one which I have to use ? Right? Please confirm ??

Thank you

Regards Chanderkant

[GenoMax]

@st.ph.n makes this clear right above your comment.

[ATpoint]

From above:

Yes, the sorted bam file.