STAR with fasta files

[Zoe Ward]

Hi Alex,

I have run the two pass mapping with a bunch of samples as standard (so I have the two genomes generated already).

I now have two FASTA files with about 1000 transcripts that I want to map back with STAR. 

I ran the commands form the second pass mapping point for the two files with:

STAR2 --runThreadN 5 --genomeDir $genome2 --readFilesIn $dir$file \

 --outFilterType BySJout --outSAMstrandField intronMotif \

--outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 20 --alignSJoverhangMin 8  --alignSJDBoverhangMin 1 \

--outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 \

--alignMatesGapMax 1000000 --outFileNamePrefix $file

The bam files that are generated for the two files say that there are only 2 and 3 input reads.

Can you help me out where I'm going wrong??

Thanks in advance,

Zoe.

[Alexander Dobin]

Hi Zoe,

are these transcripts long - longer than 500b?

In this case you would need to use STARlong - this is a separate executable that you can make with

$ make STARlong,

or use the pre-compiled binaries in the STAR bin directory.

Please check this thread for parameter recommended for mapping long reads with STARlong:

https://groups.google.com/d/msg/rna-star/E2eevlGWFbQ/JKoh4IxDBwAJ

Cheers

Alex

[Zoe Ward]

Hi Alex,

Thanks for that.

I'm a little confused as to what I use for the genomeDir argument?? Do I use the directory that I have from the 'standard' two pass method??

[Alexander Dobin]

Hi Zoe,

yes, STARlong uses the same genome index as the standard STAR.

Cheers

Alex