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Hello,
I need to convert some public bisulfite data to a SAM file so that I can visualize it with IGV. It seems that the file provided is some kind of maq file (an example is shown below). When I try to use maq2sam to convert to SAM, I get the message "maq2sam not working, need to convert with mapass2maq first." Then when I use mapass2maq I get the message "Segmentation fault." Is there anyway to convert this file to SAM format? I have attached a word document that contains how the authors processed the bisulfite data.
HWUSI-EAS455_0012:8:85:1220:291#0/1 Chloroplast 1 + 0 0 93 93 93 0 0 1 0 61 ATggGTgAATGATGggaATTgAATTTGTgATGGTGAATTTATAaTTTATTGTTTTAATTTA BB9;<?:AAB?ACB4,:BB@2=@AC@B?;AB<=<@?BCCBBA>8BBBBCA?ABBBCACBAB
HWUSI-EAS455_0012:8:9:1470:1447#0/1 Chloroplast 1 + 0 0 86 86 86 5 63 1 0 62 ATGGGTGAATGATGGGAATTGAATTTGTGGtGGtGgaTTTataatTTaTtttTTTtaTTTtT BCCBC@C?BCCBCCACB@CCBAACBCB@CA9B@(<&7=BB54&68A=/A
9BB?(2@C@.<
HWUSI-EAS455_0012:8:13:923:1108#0/1 Chloroplast 1 + 0 0 95 95 95 0 0 1 0 62 ATGGGtGAATGaTGGGAaTTGAATTTGTGATGGTGAATTTATaATTTaTTgTTTTAATTTAT BCCCC9CCBCB8BCCB?+ABBCCCCBBAC?C@CBC==CCCCB8>CC@8>@+>CCBB?CCBBA
HWUSI-EAS455_0012:8:24:816:511#0/1 Chloroplast 1 + 0 0 98 98 98 1 30 1 0 62 ATGGGTGAATGATGGGAATTGAATTTGTGATGGTGAATTTATAATTTATTGTTTTAGTTTAT BCCCC@C?BCCBCCBBA@BCBABCCCC@B?CCC<CBBCBBBBA?BBCACBBABCB?B>BC?B
HWUSI-EAS455_0012:8:30:61:176#0/1 Chloroplast 1 + 0 0 90 90 90 1 6 1 0 62 ATGgGtGAATgaTGGGAaTTgaATTTGtGATggggaATTTATAATTTATTgTTTTaaTTTAT BB@:>5ABA=06BA>?A;A<0:ACCAA:=AB81';/>AA=AB@@AAB>AB3@BA@:6BBB>A
HWUSI-EAS455_0012:8:30:234:129#0/1 Chloroplast 1 + 0 0 99 99 99 0 0 1 0 62 ATGGGTGAATGATGGGAATTGAATTTGTGATGGtGAATTTATAATTTATTGTTTTAATTTAT BCCBB@CBCBCBBB@B@ACC>BBCCCC?CBCBB7B@BCBB@BBBCBB@BCA?BCAA>BB<<@
Thank you,
Marisa
I need to convert some public bisulfite data to a SAM file so that I can visualize it with IGV. It seems that the file provided is some kind of maq file (an example is shown below). When I try to use maq2sam to convert to SAM, I get the message "maq2sam not working, need to convert with mapass2maq first." Then when I use mapass2maq I get the message "Segmentation fault." Is there anyway to convert this file to SAM format? I have attached a word document that contains how the authors processed the bisulfite data.
HWUSI-EAS455_0012:8:85:1220:291#0/1 Chloroplast 1 + 0 0 93 93 93 0 0 1 0 61 ATggGTgAATGATGggaATTgAATTTGTgATGGTGAATTTATAaTTTATTGTTTTAATTTA BB9;<?:AAB?ACB4,:BB@2=@AC@B?;AB<=<@?BCCBBA>8BBBBCA?ABBBCACBAB
HWUSI-EAS455_0012:8:9:1470:1447#0/1 Chloroplast 1 + 0 0 86 86 86 5 63 1 0 62 ATGGGTGAATGATGGGAATTGAATTTGTGGtGGtGgaTTTataatTTaTtttTTTtaTTTtT BCCBC@C?BCCBCCACB@CCBAACBCB@CA9B@(<&7=BB54&68A=/A
9BB?(2@C@.<HWUSI-EAS455_0012:8:13:923:1108#0/1 Chloroplast 1 + 0 0 95 95 95 0 0 1 0 62 ATGGGtGAATGaTGGGAaTTGAATTTGTGATGGTGAATTTATaATTTaTTgTTTTAATTTAT BCCCC9CCBCB8BCCB?+ABBCCCCBBAC?C@CBC==CCCCB8>CC@8>@+>CCBB?CCBBA
HWUSI-EAS455_0012:8:24:816:511#0/1 Chloroplast 1 + 0 0 98 98 98 1 30 1 0 62 ATGGGTGAATGATGGGAATTGAATTTGTGATGGTGAATTTATAATTTATTGTTTTAGTTTAT BCCCC@C?BCCBCCBBA@BCBABCCCC@B?CCC<CBBCBBBBA?BBCACBBABCB?B>BC?B
HWUSI-EAS455_0012:8:30:61:176#0/1 Chloroplast 1 + 0 0 90 90 90 1 6 1 0 62 ATGgGtGAATgaTGGGAaTTgaATTTGtGATggggaATTTATAATTTATTgTTTTaaTTTAT BB@:>5ABA=06BA>?A;A<0:ACCAA:=AB81';/>AA=AB@@AAB>AB3@BA@:6BBB>A
HWUSI-EAS455_0012:8:30:234:129#0/1 Chloroplast 1 + 0 0 99 99 99 0 0 1 0 62 ATGGGTGAATGATGGGAATTGAATTTGTGATGGtGAATTTATAATTTATTGTTTTAATTTAT BCCBB@CBCBCBBB@B@ACC>BBCCCC?CBCBB7B@BCBB@BBBCBB@BCA?BCAA>BB<<@
Thank you,
Marisa