Input Data

Input Data

FinaleToolkit is compatible with almost any paired-end sequence data.

BAM

A Binary Alignment Map (BAM) file provides the same information as a SAM file but in a binary format. This can save space on disk but is not human-readable.

FinaleToolkit requires that BAM files be BAI indexed. Therefore, you should have an associated .bam.bai file in the same directory as your input data.

CRAM

A Compressed Read Alignment Map (CRAM) file is a compressed version of a SAM file. It is a binary file that is smaller than a BAM file but still contains all the same information.

FinaleToolkit requires that CRAM files be CRAI indexed. Therefore, you should have an associated .cram.crai file in the same directory as your input data.

Fragment File

A fragment file (.frag.gz or frag.tsv.bgz) is derived from information in a BAM file. It is a block-gzipped BED3+2 file (similar to a tab-separated value file) that contains the following columns (with one row entry for each fragment): chrom, start, stop, mapq, and strand.

• mapq: The mapping quality of the fragment.
• strand: The strand of the fragment, which can be either + or -.

FinaleToolkit requires that fragment files be Tabix indexed. Therefore, you should have an associated .frag.gz.tbi file in the same directory as your input data. We encourage you to use our comprehensive database, FinaleDB, to access relevant fragment files. Learn more about FinaleDB here.

Example Fragment File

#chrom    start    stop    mapq    strand
chr1    10000    10050    60    +
chr1    10050    10100    60    -
chr1    10100    10150    60    +
chr1    10150    10200    60    -
chr1    10200    10250    60    +
chr1    10250    10300    60    -
chr1    10300    10350    60    +
chr1    10350    10400    60    -
chr1    10400    10450    60    +
chr1    10450    10500    60    -