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bigwigCompare bigwigCompare --bigwig1 Bigwig file --bigwig2 Bigwig file This tool compares two bigWig files based on the number of mapped reads. To compare the bigwig files, the genome is partitioned into bins of equal size, then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference. Show
sickle sickle se -t [solexa|illumina|sanger] -f input_reads.fastq -o output_reads_trimmed.fastq Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5'-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely (or replaced with an "N" record). 5'-end trimming can be disabled. Show
multiBamSummary multiBamSummary BED-file --BED selection.bed --bamfiles file1.bam file2.bam -out results.npz This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files). The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted. Alternatively, an interval file with pre-defined genomic regions can be provided. Show
bigwigCompare bigwigCompare [--numberOfProcessors INT] [--verbose] --outFileName FILENAME [--outFileFormat {bigwig,bedgraph}] This tool compares two bigWig files based on the number of mapped reads. To compare the bigwig files, the genome is partitioned into bins of equal size, then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference. Show
multiBamSummary multiBamSummary bins --bamfiles file1.bam file2.bam -out results.npz This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files). The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted. Alternatively, an interval file with pre-defined genomic regions can be provided. Show
maq maq bfq2fastq in.read.bfq out.read.fastq Convert Maq’s BFQ format to standard FASTQ format. Show
multiBamSummary multiBamSummary [-h] [--version] This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files). The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted. Alternatively, an interval file with pre-defined genomic regions can be provided. Show
bowtie-build bowtie-build [options]* <reference_in> <ebwt_base> bowtie-build builds a Bowtie index from a set of DNA sequences. bowtie-build outputs a set of 6 files with suffixes .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt. (If the total length of all the input sequences is greater than about 4 billion, then the index files will end in ebwtl instead of ebwt.) These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence files are no longer used by Bowtie once the index is built. Show
Trimmomatic java -jar <path to trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] [-trimlog <logFile>] >] [-basein <inputBase> | <input 1> <input 2>] [-baseout <outputBase> | <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ... or java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticPE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] [-basein <inputBase> | <input 1> <input 2>] [-baseout <outputBase> | <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ... Trimmomatic performs a variety of useful trimming tasks for illumina paired-end data. Show
Trimmomatic java -jar <path to trimmomatic jar> SE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input> <output> <step 1> ... or java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticSE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input> <output> <step 1> ... Trimmomatic performs a variety of useful trimming tasks for illumina single ended data. Show
maq maq fastq2bfq [-n nreads] in.read.fastq out.read.bfq|out.prefix Convert reads in FASTQ format to Maq’s BFQ (binary FASTQ) format. Show
bigwigCompare bigwigCompare [--scaleFactors SCALEFACTORS] [--pseudocount PSEUDOCOUNT] This tool compares two bigWig files based on the number of mapped reads. To compare the bigwig files, the genome is partitioned into bins of equal size, then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference. Show
samtools samtools rmdup [-sS] <input.srt.bam> <out.bam> Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads Show
bigwigCompare bigwigCompare [--blackListFileName BED file [BED file ...]] This tool compares two bigWig files based on the number of mapped reads. To compare the bigwig files, the genome is partitioned into bins of equal size, then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference. Show
bigwigCompare bigwigCompare [-h] [--version] [--binSize INT bp] This tool compares two bigWig files based on the number of mapped reads. To compare the bigwig files, the genome is partitioned into bins of equal size, then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference. Show
maq maq fasta2bfa in.ref.fasta out.ref.bfa Convert sequences in FASTA format to Maq’s BFA (binary FASTA) format. Show
bigwigCompare bigwigCompare [--deepBlueTempDir DEEPBLUETEMPDIR] [--deepBlueKeepTemp] This tool compares two bigWig files based on the number of mapped reads. To compare the bigwig files, the genome is partitioned into bins of equal size, then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference. Show
correctGCBias correctGCBias -b file.bam --effectiveGenomeSize 2150570000 -g mm9.2bit --GCbiasFrequenciesFile freq.txt -o gc_corrected.bam [options] This tool corrects the GC-bias using the method proposed by [Benjamini & Speed (2012). Nucleic Acids Research, 40(10)]. It will remove reads from regions with too high coverage compared to the expected values (typically GC-rich regions) and will add reads to regions where too few reads are seen (typically AT-rich regions). The tool computeGCBias needs to be run first to generate the frequency table needed here. Show
maq maq sol2sanger in.sol.fastq out.sanger.fastq Convert Solexa FASTQ to standard/Sanger FASTQ format. Show
bigwigCompare bigwigCompare [--region CHR:START:END] This tool compares two bigWig files based on the number of mapped reads. To compare the bigwig files, the genome is partitioned into bins of equal size, then the scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference. Show