What type of File is this? groHMM tutorial input says bam but it doesn't look bam

Question

[gocougs]

Hi.

I am trying to use groHMM to analyze GRO-seq data. I followed their tutorial on bioconductor and was able to get everything to work properly. When I tried this with my own data, it threw up errors. So I went to look at the raw bam files from the tutorial and they look like this.

Bam file from their tutorial. Note that this is a binary formatted file, not plain text.

n   16  chr7    12312   255 1M  *   0   0   *   *
n   16  chr7    12317   255 1M  *   0   0   *   *
n   16  chr7    15791   255 1M  *   0   0   *   *
n   16  chr7    15791   255 1M  *   0   0   *   *
n   16  chr7    15791   255 1M  *   0   0   *   *
n   16  chr7    15791   255 1M  *   0   0   *   *
n   16  chr7    15793   255 1M  *   0   0   *   *
n   16  chr7    15793   255 1M  *   0   0   *   *
n   16  chr7    30670   255 1M  *   0   0   *   *
n   16  chr7    30670   255 1M  *   0   0   *   *
n   16  chr7    31059   255 1M  *   0   0   *   *
n   16  chr7    31065   255 1M  *   0   0   *   *
n   16  chr7    31069   255 1M  *   0   0   *   *
n   16  chr7    31069   255 1M  *   0   0   *   *
n   16  chr7    41620   255 1M  *   0   0   *   *
n   16  chr7    143075  255 1M  *   0   0   *   *
n   16  chr7    143082  255 1M  *   0   0   *   *
n   16  chr7    143114  255 1M  *   0   0   *   *
n   16  chr7    143863  255 1M  *   0   0   *   *
n   16  chr7    143863  255 1M  *   0   0   *   *

As compared to a more traditional bam file I am familiar with.

SRR5364096.1    4   *   0   0   *   *   0   0   NAAAAACATGGTACAGTGAGTGAATATACCCCCATCCCCAAAAAAAAAAAN #0<FFFFFFFFFFIIFFIFIFF<BFFIFFIFIIIIIIIIIIIIIIIIIFFF
SRR5364096.2    0   chr17   66032340    25  51M *   0   0   TTAGGCCCCGGGGGTGGCTCTGCCACCAAGTCGTAGGCGAGCGTAATAAAN BBBFFFFFFFFFFI7BFFIFIIFIFIFFFFFFFBFFFFFFBFFBBBBFBFF XT:A:U  NM:i:3  X0:i:1  X1:i:0  XM:i:3  XO:i:0  XG:i:0  MD:Z:0C46G2A0
SRR5364096.3    16  chr8    131353360   37  51M *   0   0   GATGCATTACAGCAGAAGGTAAAGTCGACACAAAACTTCCAACTGACTGCT FIFFIIFBFIFIIFIIIIIIIIFFFFFFIFIFFFFIIIFFFFFFFFFFBBB XT:A:U  NM:i:0  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:51

So I figured that this is probably where the problem lies. What is the difference between these two BAM file types and how can I make my bam file look like the one from the tutorial?

Thanks a million,

Simon

Answer 1

[Pierre Lindenbaum]

Bam file from their tutorial. Note that this is a binary formatted file, not plain text.

it's a SAM file without any header. All reads are named 'n' and have sam flag 16: single end mapped on reverse strand, mapq=255 (=undetermined)