Is STAR aligner recommended for use with ChIP-seq data? I am trying to use STAR for ChIP-seq data to obtain reads mapped to multiple regions of the genome with mismatch options, which STAR seems to do better than Bowtie2. I get only around 14% of reads mapped, and around 80% in "% of reads unmapped: too short". From the suggestions in the link -
https://groups.google.com/forum/#!topic/rna-star/E_mKqm9jDm0, I tried --alignIntronMax 1 option but the results are similar. Please advise, thank you.
"too short" is STAR's euphemism for reads that just fail to align. What's the alignment rate you're getting with bowtie2? Chip-Seq is very tricky experimentally, so it happens quite often that libraries are full of adapter sequences etc. Aligners (as long as you are using a well-supported modern one, like bwa, bowtie2, or STAR) should not matter all that much.
Some types (e.g. H3K9me3) are also enriched for multimapping reads because these marks are enriched in heterochromatin.