Unique and multipleUnique in wig files

[Assa Yeroslaviz]

Hi,

As far as I undestand it, STAR creates two wig files, one for the unique and one for the muti-mapped reads.

I am running STAR with the parameter '--outFilterMultimapNmax 15', so I allow STAR to map reads with occurrences up to 15 times.

For this i have two questions:

1. how does STAR handle these multi-mapped reads?
Does it map them in only one position (like tophat2), or does it map them at all 15 (or whatever value I uses) different positions?

2. What reads are taken into the Unique and UniqueMultiple wig files?
If I allow reads up to 15 possibilities to be mapped, are they all being also counted into the Unique wig file, or does the Unique wig files contains only(!) unique reads regardless of the number of allowed multimapping?

Thanks in advance
Assa

[Alexander Dobin]

Hi Assa,

STAR output all alignments of multi-mapping reads, if a read maps to <= --outFilterMultimapNmax loci.

However, this filter determines just the upper boundary for the number of allowed loci, it does not force STAR to output --outFilterMultimapNmax alignments for every read.

The --outFilterMultimapScoreRange parameter controls which alignments of a read are "worthy" - all alignments with align scores (AS field in the SAM file) within this range of the top score.

No alignments are output for reads mapping to > --outFilterMultimapNmax loci.

Unique wig files contain only the reads that map to one locus, independent of --outFilterMultimapNmax.

UniqueMultiple will contain all reads that map to <= --outFilterMultimapNmax loci, however, the contribution of the reads is divided by the number of loci it maps to, i.e. the multi-mappers signal is spread equally over all loci.

Cheers

Alex

[Assa Yeroslaviz]

Hi Alex,

thanks for the answer. This raise though two questions from my side.

1. Do i understand it correctly, that if I use --outFilterMultimapNmax=1 I  the UniqueMultiple and Unique output files will be identical? What is happening with all the reads that have reads > outFilterMultimapNmax? Are they also not showing in the wig file?

2. How does STAR handle multi-mappers? Are they being mapped to all possible positions, or only to one specific / by chance?

thanks again

Assa

[Alexander Dobin]

Hi Assa,

>>>Do i understand it correctly, that if I use --outFilterMultimapNmax=1 I  the UniqueMultiple and Unique output files will be identical? 

yes

>>>What is happening with all the reads that have reads > outFilterMultimapNmax?

these reads are considered unmapped and do not show in BAM or wiggles.

>>>How does STAR handle multi-mappers? Are they being mapped to all possible positions, or only to one specific / by chance?

All loci that STAR could find with the score within the --outFilterMultimapScoreRange range of the best score are output.

Cheers

Alex