Hello, I downloaded some files from GSE42880, as you can see from the original GEO data, the data are in .bam.wig.gz format. I am quite confused by this format and try to convert everything to .bam file. I searched online, every question I found are to convert .bam to .wig, and not the reverse way. Could anyone give me some suggestion? Thanks!
If they are in WIG format, you cannot convert them back to BAM. WIG isn't just an alternate format that contains the same information as a BAM file, it's a format for representing the strength of a signal, such as the depth of reads, across the genome. It doesn't contain the information needed to convert back to a BAM file.
To illustrate Colin's point here are typical lines from a WIG file:
chrI 10 20 1.5
chrI 20 30 1.7
chrI 30 40 2.0
chrI 40 50 1.8
And these are typical lines from a BAM file:
ERR458493.552967 16 chrI 140 255 12M61232N37M2S * 0 CCACTCGTTCACCAGGGCCGGCGGGCTGATCACTTTATCGTGCATCTTGGC BB?HHJJIGHHJIGIIJJIJGIJIJJIIIGHBJJJJJJHHHHFFDDDA1+B NH:i:1 HI:i:1 AS:i:41 nM:i:2
ERR458498.814362 0 chrI 1593 255 11M71474N40M * 0 TTTCTACAAAGATTCTCTCACTTGTACAGAGGTGTCTTCCCATTCGTTTTC CCCFFFFFHHHHHJJGIJJJIJJIHJJJIJJJHHIJJJJJJJIJJJGIJIG NH:i:1 HI:i:1 AS:i:43 nM:i:2
ERR458496.427513 16 chrI 3782 255 51M * 0 0 CAGTAAAGGCTTGGTAGTAACCATAATATTACCCAGGTACGAAACGCTAAG JJJJIJJJJIJJJJJJJJJIJJJJJJJJGHBJJJJJJJHHHHHFFFFFCCB NH:i:1 HI:i:1 AS:i:50 nM:i:0
ERR458493.243111 0 chrI 3873 255 51M * 0 0 TGAAAATATTCTGAGGTAAAAGCCATTAAGGTCCAGATAACCAAGGGACAA @@<DDDDEH<<<CEFHAEIHHGGCHIGEEGG?@FF@<?ECGGGIIHIIIII NH:i:1 HI:i:1 AS:i:50 nM:i:0
ERR458494.816646 16 chrI 3972 255 51M * 0 0 TAATGAGCTAGTGATCCGGAAAGCTACTTTATGATGTTTCAAGGCCTGAAG @BBEBG;IGFDD@C:BHC<4A?94C<CH<EEEFABBFE<CDCBBD;DD=?1 NH:i:1 HI:i:1 AS:i:50 nM:i:0
ERR458497.736781 16 chrI 3976 255 51M * 0 0 GAGCTAGTGATCCGGAAAGCTACTTTATGATGTTTCAAGGCCTGAAGTTTG IJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJJHHHHHFFFFFCCC NH:i:1 HI:i:1 AS:i:50 nM:i:0
As you can see, the WIG format simply contains some sort of value per (arbitrarily sized) windows of a given genome. These values can be, for example, normalized read coverages. BAM files, however, contain detailed information about every single read including a read's sequence, its alignment score and so on.
Looks like the original fastq files are available. Download, align and make your own BAM files.
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version 2.3.6
trying to convert wig to bam is like creating a cow from a steak