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Genome guided assembly with Trinity using STAR genome index

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

rna-seq star trinity
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updated by ChanderKant (CK) Chaudhary • ChanderKant (CK) Chaudhary • written by nikelle.petrillo nikelle.petrillo

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
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written by st.ph.n st.ph.n

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

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written by nikelle.petrillo nikelle.petrillo

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.

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written by st.ph.n st.ph.n

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

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written by ChanderKant (CK) Chaudhary • ChanderKant (CK) Chaudhary

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

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written by GenoMax GenoMax

From above:

Yes, the sorted bam file.

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written by ATpoint ATpoint

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