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Anna Battenhouse

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Sub-commandDescriptionUse case(s)
bamtobedConvert BAM files to BED format.You want to have the contig, start, end, and strand information for each mapped alignment record in separate fields. Recall that the strand is encoded in a BAM flag (0x10) and the exact end coordinate requires parsing the CIGAR string.
bamtofastqExtract FASTQ sequences from BAM alignment records.You have downloaded a BAM file from a public database, but it was not aligned against the reference version you want to use (e.g. it is hg18 and you want an hg38 alignment). To re-process, you need to start with the original FASTQ sequences.
getfastaGet FASTA entries corresponding to regions.Preparation You want to run motif analysis, which requires the original FASTA sequences, on a set of regions of interest. You   In addition to the BAM file, you must provide FASTA file(s) for the genome/reference used for alignment (e.g. the FASTA file used to build the aligner index).
coverageCompute genome-wide coverage of your regsionsregions; generate per-base genome-wide signal trace.
  • You have performed a WGS (whole genome sequencing) experiment and want to know if has resulted in the desired coverage depth.
  • Calculate what proportion of the (known) transcriptome is covered by your RNA-seq alignments. Provide the transcript regions as a BED or GFF/GTF file.
  • Produce a per-base genome-wide signal (in bedGraph format) for a ChIP-seq or ATAC-seq experiment. After conversion to binary bigWig format, such tracks can be configured in the UCSC Genome Browser as custom tracks.
multicovCount overlaps between one or more BAM files and a set of regions of interest.
  • Count RNA-seq alignments that overlap a set of genes of interest. While this task is usually done with a specialized RNA-seq quantification tool (e.g. DESeq2 featureCounts or EdgeR HTSeq), bedtools multicov can provide a quick estimate, e.g. for QC purposes.
mergeCombine a set of possibly-overlapping regions into a single set of non-overlapping regions.Collapse overlapping gene annotations into per-strand non-overlapping regions before counting (e.g with featureCounts or HTSeq). If this is not done, the source regions will potentially be counted multiple times, once for each (overlapping) target region it intersects.
subtractRemove unwanted regions.Remove rRNA gene regions from a merged gene annotations file before counting.
intersectDetermine the overlap between two sets of regions.Similar to multicov, but takes BED files as input and can also report (not just count) the overlapping regions.
closestFind the genomic features nearest to a set of regions.For a set of significant ChIP-seq transcription factor (TF) binding regions ("peaks") that have been identified, determine nearby genes that may be targets of TF regulation.

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