Hello

 I am wondering if there is some package to detect str in a Bam file. I have found some things for RNA, but I don't know if they also can be used for DNA

thanks

Hi,

I don't know if there is any Bioconductor package for detecting short tandem repeats in a BAM file. Note that you could try to do this on the FASTQ files (containing the read sequences before alignment) instead of the BAM file. FWIW here is a home-made solution that builds on top of the findTandemRepeats() function from the A: Is there any package helps finding Tandem Repeats ? post:

## Return the index of sequences in DNAStringSet object 'x' that
## contain repeat tandems.
detectTandemRepeats <- function(x)
{
    big_subject <- unlist(xscat(x, "-"), use.names=FALSE)
    tr_ranges_on_big_subject <- ranges(
        findTandemRepeats(big_subject, include.period1=TRUE)
    )
    x_ranges_on_big_subject <- successiveIRanges(width(x),
                                                 gapwidth=1L)
    hits <- findOverlaps(tr_ranges_on_big_subject,
                         x_ranges_on_big_subject)
    q_hits <- queryHits(hits)
    s_hits <- subjectHits(hits)
    ## A sanity check.
    stopifnot(
        all(start(tr_ranges_on_big_subject)[q_hits] >=
            start(x_ranges_on_big_subject)[s_hits]),
        all(end(tr_ranges_on_big_subject)[q_hits] <=
            end(x_ranges_on_big_subject)[s_hits]))
    unique(s_hits)
}

Then:

library(GenomicAlignments)
library(RNAseqData.HNRNPC.bam.chr14)
file <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1]
gal <- readGAlignments(file, use.names=TRUE, param=ScanBamParam(what="seq"))
seq <- mcols(gal)$seq
names(seq) <- names(gal)
seq
#  A DNAStringSet instance of length 800484
#          width seq                                          names               
#      [1]    72 TGAGAATGATGATTTCC...TTTTTTATGGCTGCAT ERR127306.26333541
#      [2]    72 CCCATATGTACATCAGG...CAGTTGGATACACACA ERR127306.12926170
#      [3]    72 CCCCAGGTATACACTGG...TCAAGGTGGACACCAG ERR127306.12926170
#      [4]    72 CATAGATGCAAGAATCC...AAAAGATAACTTACCA ERR127306.26974899
#      [5]    72 TAGCACACTGAATTCAA...TTACCCCAAGGATACA ERR127306.26974899
#      ...   ... ...
# [800480]    72 GAAATTGCTGAAACTTG...GAGTACATCACATCAG ERR127306.3567919
# [800481]    72 CAAAGCTGGATGTGTCT...GTGTGGTTTTGCTGCC ERR127306.21510817
# [800482]    72 GTGTGGTTTTGCTGCCC...AGGCACATTAATTTTC ERR127306.21510817
# [800483]    72 AAGGAACCCTTGAACTC...GGTCCTCTGCCTCAAG ERR127306.661203
# [800484]    72 CATGACTTGATGGCTGG...TTGCCATACAGTATTT ERR127306.661203
tandem_repeat_idx <- detectTandemRepeats(seq)

tandem_repeat_idx now contains the index of alignments in gal with repeat tandems. To see the details:

findTandemRepeats(seq[[tandem_repeat_idx[1]]], include.period1=TRUE)
#   Views on a 72-letter DNAString subject
# subject: CTGTCTCAAAAACAAACAAACCAAAATAAT...GATGATGATGACTGCAATGAGCAGGTGCAC
# views:
#     start end width
# [1]    29  53    25 [ATGATGATGATGATGATGATGATGA]

findTandemRepeats(seq[[tandem_repeat_idx[2]]], include.period1=TRUE)
#   Views on a 72-letter DNAString subject
# subject: ATTTTGAAGCCCCAGGAATATGTGTGTGTG...TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
# views:
#     start end width
# [1]    39  72    34 [TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG]

findTandemRepeats(seq[[tandem_repeat_idx[3]]], include.period1=TRUE)
#   Views on a 72-letter DNAString subject
# subject: CACACACACACACACACACACACACACACA...TGTTTCTCCAGGCTTGGTCCCTGGGACCGT
# views:
#     start end width
# [1]     1  31    31 [CACACACACACACACACACACACACACACAC]

## etc...

Cheers,

H.

Hi

 Thanks for the answer, it will be useful

pau

Hi

 Thanks for the answer, it will be useful

pau

Hi

 Thanks for the answer, it will be useful

pau

Hi

 Thanks for the answer, it will be useful

pau