which mapping program is good for RainDance Data

[JCYAO]

I have a set of target resequencing data obtained from RainDance. Anyone knows which mapping program is good for this type of data? Is it still good to use BWA?

Thanks

[krobison]

Which sequencing platform? What was done to the amplicons to prepare them for sequencing? I think those are two critical questions.

In general, it isn't obvious why RainDance data would map differently. The one thing I have heard anecdotally with targeted sequencing (I'd love to find this in print somewhere) is that it is a huge mistake to map only against your target regions -- map against the entire genome. Otherwise, the aligner may force things to fit that are really off-target (in their presentations & publication, RainDance has remarked on carry-over DNA showing up in the sequencing data)

[nilshomer]

Which sequencing platform? What was done to the amplicons to prepare them for sequencing? I think those are two critical questions.

In general, it isn't obvious why RainDance data would map differently. The one thing I have heard anecdotally with targeted sequencing (I'd love to find this in print somewhere) is that it is a huge mistake to map only against your target regions -- map against the entire genome. Otherwise, the aligner may force things to fit that are really off-target (in their presentations & publication, RainDance has remarked on carry-over DNA showing up in the sequencing data)

For targeted sequencing we usually align the data twice: once to the target regions and once to the whole genome. Using your favorite aligner should be no problem given the data is of good quality.

[krobison]

For targeted sequencing we usually align the data twice: once to the target regions and once to the whole genome. Using your favorite aligner should be no problem given the data is of good quality.

How often have you seen a difference in the results? Is it usually around repeats/close paralogs or something else?

[JCYAO]

For targeted sequencing we usually align the data twice: once to the target regions and once to the whole genome. Using your favorite aligner should be no problem given the data is of good quality.

How do you align the data to the target regions? I have the target region bed file as follows

chr start pos end pos
chr5 112100483 112101521
chr5 112118469 112118621
chr5 112129922 112130006
chr5 112130785 112130986
chr5 112139225 112139333
chr5 112144386 112144499
...

how to generate a fasta file for the target regions so I can map reads to the target regions?

Thanks

[nilshomer]

How do you align the data to the target regions? I have the target region bed file as follows

chr start pos end pos
chr5 112100483 112101521
chr5 112118469 112118621
chr5 112129922 112130006
chr5 112130785 112130986
chr5 112139225 112139333
chr5 112144386 112144499
...

how to generate a fasta file for the target regions so I can map reads to the target regions?

Thanks

For BFAST (I am the author), you can input a list of of regions when creating the indexes ('bfast index -x'). Other alignment software may have similar capabilities, or you may have to create a custom FASTA file.