Category

Multiple sequence alignments / Conservation


Usage

mafsInRegion regions.bed out.maf|outDir in.maf(s)


Manual

This tool is part of UCSC Genome Browser's utilities.

Required arguments

  • regions.bed: Path to a bed file which stores all the regions that you want to extract
  • out.maf | outDir: Output file name or Output folder path
  • in.maf(s): Path to the input MAF file

Options

  • -outDir: output separate files named by bed name field to outDir
  • -keepInitialGaps: keep alignment columns at the beginning and of a block that are gapped in all species

Example

Assume you have a set of ChIP-seq peaks in a bed file called peaks.bed (corresponds to the first positional argument regions.bed):

$ head peaks.bed
chr1    9740    10540    CTCF_1.294
chr1    10901    11701    CTCF_2.954
chr1    15866    16666    CTCF_3.40
chr1    25692    26492    CTCF_4.78
chr1    91003    91803    CTCF_5.199
chr1    104574    105374    CTCF_6.51
chr1    138816    139616    CTCF_7.75
chr1    237350    238150    CTCF_8.435
chr1    250914    251714    CTCF_9.52
chr1    324692    325492    CTCF_10.64

Assume you have the multiple alignments for 46 organisms from UCSC, and the files are stored in a folder called maf (corresponds to the third positional argument in.maf(s)):

$ ls maf/*.maf
maf/chr10.maf                 maf/chr23_KZ114986v1_alt.maf  maf/chr4.maf
maf/chr11.maf                 maf/chr23_KZ115679v1_alt.maf  maf/chr5_KZ115115v1_alt.maf
maf/chr12.maf                 maf/chr23_KZ115681v1_alt.maf  maf/chr5.maf
maf/chr14.maf                 maf/chr23_KZ115682v1_alt.maf  maf/chr6.maf
maf/chr15.maf                 maf/chr23_KZ115692v1_alt.maf  maf/chr7_KZ115231v1_alt.maf
maf/chr16.maf                 maf/chr23.maf                 maf/chr7.maf
maf/chr17_KZ115524v1_alt.maf  maf/chr24_KZ115712v1_alt.maf  maf/chr8_KZ115269v1_alt.maf
maf/chr17.maf                 maf/chr24_KZ115722v1_alt.maf  maf/chr8.maf
maf/chr18.maf                 maf/chr24.maf                 maf/chr9_KZ114904v1_alt.maf
maf/chr19.maf                 maf/chr25_KZ115732v1_alt.maf  maf/chr9_KZ115282v1_alt.maf
maf/chr1_KZ115007v1_alt.maf   maf/chr25.maf                 maf/chr9.maf
maf/chr1.maf                  maf/chr2.maf                  maf/chrM.maf
maf/chr21.maf                 maf/chr3_KZ115071v1_alt.maf   maf/chrUn_KN150185v1.maf
maf/chr22.maf                 maf/chr3.maf

You can use mafsInRegion to extract multiple sequence alignment within ChIP-seq peaks and save the extracted alignments to a file called output.maf (corresponds to the second positional argument out.maf):

mafsInRegion peaks.bed output.maf maf/*.maf

The above command writes content like the following to the output file:

$ head output.maf
##maf version=1 scoring=blastz
a score=0.000000
s danRer11.chr10 21784387 800 + 45420867 TTAGATGTGAATGATAATGCACCTGAGATCATCATCACATCCTCACCCAAACCTGTGCGAGAAGATGCGCCTGCTGGGACAATGGTAGCTTTAATAAACGTTAAAGATTTAGATTCGGGCATAAACGGGAACGTAACTCTTCTTATTTTATCTGATACTCCTTTTAAATTAAAGCCAACATTTGCAAACCATTACGCACTGGTAACAGATTCAAAATTAGATCGAGAAAAGTTTCCTAAATATGACATTGAGCTTAAAGCATCAGACTCTGGATCACCTCCACTGGTATCAAGCAAACTCA--TTACAGTTAATATACTAGATGTCAATGATAATCCTCCTGTTTTCTCTGAACGTGTGTACTCGGTTTACATTAAAGAAAACAGCGCTCCAGGATCGATATTAGCATCGGTGACAGCATCAGATCTAGATACAGGAGAAAATGCAAAAATTGTGTATTCAGTTATTGATACTAATACTCGAGACGTACCTGTCTCTTCCTATGTATACATAAACGCAGAAAATGGCAGTATATTTAGCATGCACTCGTTTGATTACGAGAAAAT-AAAGGTCT-----TTCATGTTATTGTGCTTGCCAAAGATCAAGGCTCCCAATCTCTGAGCAGCAACGCTACTGTTCATGTATTTATTCTGGACCAGAACGATAATGCACCTGCTGTCATTTACCCGTCCACATCCATGGGCTCGGTCTCTAAT-CAGAGGA-----TGCCCCGTTCTGCTAAAGCAGGACATCTCGTTACTAAGGTAACGGCAGTGGACGCGGACTCGGGTCATAACGCCTGGCTGTT
s mm10.chr18     37767127 803 + 90702639 CTGGACGTGAACGACAATGCCCCTGAAGTAGCCATCACGTCCCTCACCAACTCTGTCCCAGAAAACTCTCCCCAAGGGACATTAATAGCACTTTTAAACGTAAATGATCAAGATTCTGGGGAAAATGGACAGGTAATCTGTTCCATCCAAGAGAATCTGCCCTTTAAGTTAGAAAAGTCTTACGGAAACTATTATAGATTAGTCACAGATGCAGTCCTGGACCGAGAAGAGGTTCCTAGTTACAACATCACAATGACCGCCACTGACAGGGGAAGTCCGCCCCTGACAACAG--AAACTCACCTCGCACTGGACATAGCAGACACGAACGATAACTCGCCCGTTTTCCTTCAGGCCTCATACTGGGCCTACATCCCAGAGAATAACCCTAGAGGGGCCTCTATCGCATCCGTGACCGCCCACGACCCCGACAGTGACAAAAATGCCCAAGTCACTTACTCCCTAGCTGAGGACACCCACCAGGGCGTGCCCCTTTCCTCTTACGTTTCCATCAACTCGGACACTGGTGTCCTGTACGCACTGCATTCCTTTGACTACGAGCAGTTCCCAGACCTACAACTGCAAGTGATAGCGCGTGACAGCGGGGA------CCCGCCACTCAGCAGCAACGTGTCACTGAGCTTGTTCGTGCTGGATCAGAATGACAACGTCCCCGAAATCTTGTACCCCACTCTCCCTACCGAC---GGTTCTACTGGAGTGGAGCTAGCACCCCGCTCAGCAGAGCCTGGCTATCTGGTGACAAAGGTGGTGGCAGTGGACAGAGACTCAGGACAGAACGCCTGGCTGTC

File formats this tool works with
MAF

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