MACS SAMfiles

khb · 12-17-2010, 06:26 AM

Hi
I've used MACS to find peaks in a SAM file, and I got a line in the peaks.bed file in SAM with negative start (-98) so I cannot upload the file in UCSC genome browser.
chrM -98 4052 macs_PEAK_50677 971.81
Does somebody understand the reason for this output? Is there a bug in MACS when it finds hits the negative strand?
Thanks

polyatail · 12-17-2010, 02:01 PM

Hi khb,

What software did you use to produce the alignment? Can you post some of the reads mapping to chrM?

Andrew

khb · 12-19-2010, 10:37 AM

I used bowtie.
Here is some of the output from bowtie
HWUSI-EAS1525_0005_FC:4:1:7582:8004#0/1 - chrM 313 CCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAA cgcag_^^^[X_LXV]ggggcfccfX_YZZQdbdb_afffdfcffggggg 0
HWUSI-EAS1525_0005_FC:4:1:15912:8129#0/1 - chrM 14456 ATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAA afhhhfhhghhhhfhhhhhhgghhhfghghhghhhhhhhhhhhhhhhhgh 0
HWUSI-EAS1525_0005_FC:4:1:13895:8331#0/1 + chrM 3185 ATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAA ggggcgggggffdcffdfffgggggggggggggggffgggfdafffeccd 0
HWUSI-EAS1525_0005_FC:4:1:10583:8537#0/1 - chrM 12329 TAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTAACTTCC gfgggggggggdgggeffefaffafadde\_d^eefffafffffcebbee 0 6:G>A
HWUSI-EAS1525_0005_FC:4:1:14677:8853#0/1 - chrM 11331 CCAACAACTTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATA ]adcffeffcffcfffcddffcfcdedeee[afcffcffcffdcffffcf 0
HWUSI-EAS1525_0005_FC:4:1:19550:9039#0/1 + chrM 3344 TTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGC hhhhhhhhhhhghghehgghhhhhghfhghhg_hhfcfefgdfffcfdcc 0
HWUSI-EAS1525_0005_FC:4:1:5655:9204#0/1 + chrM 13011 CCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCC hhhhhhghhhhhhhhhhhhghghhhgahgh_ffcchhhhfhchgghhh`h 0
HWUSI-EAS1525_0005_FC:4:1:3891:9219#0/1 - chrM 12759 CATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGAT ccffdagggggddgegffgggggggggffgffffdgfecfcggggggggg 0
HWUSI-EAS1525_0005_FC:4:1:10936:9386#0/1 - chrM 511 CCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCC c[^Y^T[T[Wb]bTbf[feeb`d_ecffdb]deeefff_fafffff`eff 0
HWUSI-EAS1525_0005_FC:4:1:5529:9413#0/1 + chrM 595 CCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATA hhhhhhghhfhhhghhhhhhhhhhhhhhhhghhhfghhhhhhhhhhhhfh 0
HWUSI-EAS1525_0005_FC:4:1:10410:9859#0/1 + chrM 10090 CCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTC gggfgfcffafffdff_fcfffddffffffggfggfa]fcfefcfaffec 0

Thanks

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12-17-2010, 06:26 AM	#1
khb Member Location: Oslo Join Date: Dec 2010 Posts: 15	MACS SAMfiles Hi I've used MACS to find peaks in a SAM file, and I got a line in the peaks.bed file in SAM with negative start (-98) so I cannot upload the file in UCSC genome browser. chrM -98 4052 macs_PEAK_50677 971.81 Does somebody understand the reason for this output? Is there a bug in MACS when it finds hits the negative strand? Thanks

12-19-2010, 10:37 AM	#3
khb Member Location: Oslo Join Date: Dec 2010 Posts: 15	I used bowtie. Here is some of the output from bowtie HWUSI-EAS1525_0005_FC:4:1:7582:8004#0/1 - chrM 313 CCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAA cgcag_^^^[X_LXV]ggggcfccfX_YZZQdbdb_afffdfcffggggg 0 HWUSI-EAS1525_0005_FC:4:1:15912:8129#0/1 - chrM 14456 ATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAA afhhhfhhghhhhfhhhhhhgghhhfghghhghhhhhhhhhhhhhhhhgh 0 HWUSI-EAS1525_0005_FC:4:1:13895:8331#0/1 + chrM 3185 ATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAA ggggcgggggffdcffdfffgggggggggggggggffgggfdafffeccd 0 HWUSI-EAS1525_0005_FC:4:1:10583:8537#0/1 - chrM 12329 TAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTAACTTCC gfgggggggggdgggeffefaffafadde\_d^eefffafffffcebbee 0 6:G>A HWUSI-EAS1525_0005_FC:4:1:14677:8853#0/1 - chrM 11331 CCAACAACTTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATA ]adcffeffcffcfffcddffcfcdedeee[afcffcffcffdcffffcf 0 HWUSI-EAS1525_0005_FC:4:1:19550:9039#0/1 + chrM 3344 TTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGC hhhhhhhhhhhghghehgghhhhhghfhghhg_hhfcfefgdfffcfdcc 0 HWUSI-EAS1525_0005_FC:4:1:5655:9204#0/1 + chrM 13011 CCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCC hhhhhhghhhhhhhhhhhhghghhhgahgh_ffcchhhhfhchgghhh`h 0 HWUSI-EAS1525_0005_FC:4:1:3891:9219#0/1 - chrM 12759 CATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGAT ccffdagggggddgegffgggggggggffgffffdgfecfcggggggggg 0 HWUSI-EAS1525_0005_FC:4:1:10936:9386#0/1 - chrM 511 CCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCC c[^Y^T[T[Wb]bTbf[feeb`d_ecffdb]deeefff_fafffff`eff 0 HWUSI-EAS1525_0005_FC:4:1:5529:9413#0/1 + chrM 595 CCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATA hhhhhhghhfhhhghhhhhhhhhhhhhhhhghhhfghhhhhhhhhhhhfh 0 HWUSI-EAS1525_0005_FC:4:1:10410:9859#0/1 + chrM 10090 CCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTC gggfgfcffafffdff_fcfffddffffffggfggfa]fcfefcfaffec 0 Thanks Last edited by khb; 12-19-2010 at 10:25 PM.

12-17-2010, 02:01 PM	#2
polyatail Member Location: New York, NY Join Date: Dec 2010 Posts: 25	Hi khb, What software did you use to produce the alignment? Can you post some of the reads mapping to chrM? Andrew