SAM, BAM, and CRAM: Alignment Maps

Note

These three file formats are closely related and collectively called “XAM” format whenever the specific format is irrelevant.

XAM file: Content format

Comparison of SAM, BAM, and CRAM formats

Format

Type

I/O Effort

I/O Time

File Size

Uses in SEISMIC-RNA

Sequence Alignment Map

text

●

●●

●●●

parsing and editing

Binary Alignment Map

binary

●●

●

●●

short-term storage

CompRessed Alignment Map

binary

●●●

●●●

●

long-term storage

  • “I/O Effort” ranks the difficulty of reading/writing the format.

  • “I/O Time” ranks the amount of time needed to read/write the format.

  • “File Size” ranks the sizes of files in the format.

See the Samtools website for more information on SAM, BAM, and CRAM.

XAM file: Endedness

Similar to read endedness in FASTQ files (see Endedness: single-end and paired-end reads), reads in XAM files are also single- or paired-end. SEISMIC-RNA also requires that each XAM file contain only single-end or only paired-end reads. Unlike with FASTQ files, paired-end XAM files must be interleaved; SEISMIC-RNA cannot process XAM files with only 1st or only 2nd mates.

XAM file: Quality score encodings

SAM files encode Phred quality scores in the same manner as FASTQ files (see Phred quality score encodings). BAM and CRAM files also encode Phred scores, but in a binary format.

XAM file: Path format

XAM file extensions

SEISMIC-RNA accepts the following extensions for XAM files:

  • SAM: .sam

  • BAM: .bam

  • CRAM: .cram

XAM path parsing

  • The file name is the reference.

  • The file must be in a directory named align.

  • The directory containing align is the sample.

For example, SEISMIC-RNA would parse project/out/umber/align/chartreuse.cram to the sample umber and reference chartreuse.

XAM file: Uses

XAM as input file

Alignment maps for the Relate step must be input as XAM files.

XAM as output file

  • The Align step outputs a file in CRAM (with option --cram) or BAM (with option --bam) format for each reference to which each sample was aligned.

XAM as temporary file

  • The Align step writes a temporary BAM file for each input FASTQ, then splits that file into one BAM/CRAM file for each reference.

  • The Relate step filters and converts each input BAM/CRAM file into a temporary SAM file, which it parses to generate the relation vectors.