放置在最前面的参考链接
支持的文件转换类型
- text file to wig
- bed to wig
- wig to bed
- wig to bigwig
- bed to bigbed
- BAM to bedGraph for UCSC genome browser
- bam to bigwig
- bed to gff
- Split bed file by chromosome
- gff to gtf
- gtf to bed
- blat to gff
- ...
由于需要翻墙,所以这里直接将整个网页复制粘贴过来(这应该不侵权吧!)
Convert text file to wig
Sample command:
txt2wig.pl foo.txt trackName(one word) > foo.wig
Convert bed to wig
Sample command:
bed2wig.pl inputBed sampleName(one word) probeWidth > outputWig
Note: It assumes that the probe width in all records is constant.
If probe width is not constant, you can use bedGraph format.
To convert bed to bedGraph format, just change the track name to bedGraph, and minus chromosome end position in bed format by 1.
Convert wig to bed
Sample command with variableStep wig format:
wig2bed.pl inputWig sampleName(one word) > outputBed
Sample command with fixedStep wig format:
wig2bed_fixedStep.pl inputWig > outputBed
Convert wig to bigwig
Sample commands:
Get chromosome lengths
fetchChromSizes hg18 > chrSize.txt
Convert wig to big wig:
wigToBigWig foo.wig chrSize.txt foo.bw
Convert bed to bigbed
Sample commands:
Get chromosome lengths
fetchChromSizes hg18 > chrSize.txt
Convert bed to big bed:
bedToBigBed foo.bed chrSize.txt foo.bb
Convert BAM to bedGraph for UCSC genome browser
To view BAM files on UCSC browser, both foo.sorted.bam and foo.sorted.bam.bai have to be on a http or ftp server. One way to get around this is to convert BAM files into bedGraph files, which should be small enough that they can be simply uploaded.
genomeCoverageBed -split -bg -ibam sorted.bam -g hg19.genome
where hg19.genome file is tab delimited and structured as follows:
<chromName><TAB><chromSize>
chr1 249250621
One can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg19.chromInfo" > hg19.genome
Convert bam to bigwig
- Method 1: Single-base resolution across the genome
Step1: convert bam to bedGraph format:
genomeCoverageBed -split -bg -ibam accepted_hits.bam -g /nfs/genomes/mouse_gp_jul_07/anno/mm9.size > accepted_hits.bedGraph
Step2: convert bedGraph to bigwig format:
bedGraphToBigWig accepted_hits.bedGraph /nfs/genomes/mouse_gp_jul_07/anno/mm9.size accepted_hits.bw
where mm9.size file is tab delimited and structured as follows:
<chromName><TAB><chromSize>
- Method 2: Resolution of desired window size (after creating windows across desired regions or genome)
coverageBed -a Human.hg19.1000.500.bed -b Sample_1.sorted.bam | cut -f1-4 > Sample_1.1000.500.coverage.bedgraph
Update/fix UCSC GTF file
- GTF files from UCSC Table Browser use RefSeq (NM* ids) for both gene_id and transcript_id which may not be compatible for some programs (eg. counting by genes using HTSeq)
- Some Refseq gtf files (such as for the hg19, hg18, mm9, and dm3 assemblies) are in /nfs/genomes/, under gtf/ in each species folder. If you would like to create additional files, here are the steps:
Step 1: Use UCSC Table Browser to download RefSeq id and gene symbol.
Use "Genes and Gene Prediction Tracks" for group, "RefSeq Genes" for track and "refGene" for table. Choose "selected fields from primary and related tables" for output format and click "get output". In the next page select "name" and "name2" for the fields.
output format should be : NM_017940 NBPF1
Step 2: Download a gtf file from the UCSC Table Browser
This uses refseq ID as gene_id and transcript_id, so we need to replace it with the gene symbol.
sample command:
/nfs/BaRC_Public/BaRC_code/Perl/fix_gtf_refSeq_ensembl.pl hg19.refgene.gtf refseq2symbol > hg19.refgene.gtf
Step 3: About 50-70 genes in the gtf file from UCSC are incorrect; they include exons with a start coordinate that is larger than the end coordinate.
Software such as cufflinks fails to deal with this situation and ignores these exons.
Since this only affects the last 1-3 bases of a transcript, a temporary solution is to remove these records.
sample command: awk -F"\t" '{ if($4<=$5) print $0 }' hg19.refgene.gtf > hg19.refgene_new.gtf
- Ensembl gtf files can be downloaded from ftp://ftp.ensembl.org/pub/current_gtf/
Convert bed to gff
- Note that bed and gff use slightly different coordinate conventions
- Use /nfs/BaRC_Public/BaRC_code/Perl/bed2gff/bed2gff.pl
USAGE: bed2gff.pl bedFile > gffFile
Ex: bed2gff.pl foo.bed WIBR exon > foo.gff
Split bed file by chromosome
- Sometimes it's easier working with only one chromosome of regions at a time
- Output files will be named like "Sample_1.chr1.bed".
awk '{close(f);f=$1}{print > "Sample_1."f".bed"}' Sample_1_all_chrs.bed
Convert gff to gtf
- Use gffread: Try 'gffread -h' too see the program's many options
gffread My_transcripts_genes.gff3 -T -E -o My_transcripts_genes.gtf
Convert gtf to bed
- convert gtf to genePhred
gtfToGenePred my.gtf my.genePhred
- convert genePhred to bed:
awk -f genePhredToBed my.genePhred > my.bed
- genePhredToBed is a awk script by Katrina Learned, downloaded from UCSC Genome Browser discussion list
#!/usr/bin/awk -f
#
# Convert genePred file to a bed file (on stdout)
#
BEGIN {
FS="\t";
OFS="\t";
}
{
name=$1
chrom=$2
strand=$3
start=$4
end=$5
cdsStart=$6
cdsEnd=$7
blkCnt=$8
delete starts
split($9, starts, ",");
delete ends
split($10, ends, ",");
blkStarts=""
blkSizes=""
for (i = 1; i <= blkCnt; i++) {
blkSizes = blkSizes (ends[i]-starts[i]) ",";
blkStarts = blkStarts (starts[i]-start) ",";
}
print chrom, start, end, name, 1000, strand, cdsStart, cdsEnd, 0, blkCnt, blkSizes, blkStarts
}
Convert blat to gff
- Use /nfs/BaRC_Public/BaRC_code/Perl/blat2gff/blat2gff.pl
Convert BLAT output file (PSL format) into GFF format (v1.1 14 Dec 2010)
blat2gff.pl blatFile dataSource(ex:WIBR) > gffFile
Create wiggle files for visualizing paired-end data mapping to the + and - strands
- split by strand by matched strand
# input: accepted_hits.bam
# output: accepted_hits_negStrand.bam: mapped to negative strand
# accepted_hits_posStrand.bam: mapped to positive strand
bsub "samtools view -f 16 -b accepted_hits.bam >| accepted_hits_negStrand.bam"
bsub "samtools view -F 16 -b accepted_hits.bam >| accepted_hits_posStrand.bam"
- split reads by pair
# input: accepted_hits_posStrand.bam or accepted_hits_negStrand.bam
# output: 1st pair: *_1stPair.bam
# 2nd pair: *_2ndPair.bam
bsub "samtools view -b -f 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_1stPair.bam"
bsub "samtools view -b -F 0x0040 accepted_hits_posStrand.bam > accepted_hits_posStrand_2ndPair.bam"
bsub "samtools view -b -f 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_1stPair.bam"
bsub "samtools view -b -F 0x0040 accepted_hits_negStrand.bam > accepted_hits_negStrand_2ndPair.bam"
- convert from bam to bedgraph format
# input: bam format: accepted_hits_*Strand_*Pair.bam
# /nfs/genomes/mouse_gp_jul_07/anno/mm9.size: length of each chromosome, format like
# chr1 197195432
# output: bedgraph format: accepted_hits_*Strand_*Pair.bedgraph
bsub "genomeCoverageBed -split -bg -ibam accepted_hits_posStrand_1stPair.bam -g mm9.size >| accepted_hits_posStrand_1stPair.bedgraph"
bsub "genomeCoverageBed -split -bg -ibam accepted_hits_posStrand_2ndPair.bam -g mm9.size >| accepted_hits_posStrand_2ndPair.bedgraph"
bsub "genomeCoverageBed -split -bg -ibam accepted_hits_negStrand_1stPair.bam -g mm9.size >| accepted_hits_negStrand_1stPair.bedgraph"
bsub "genomeCoverageBed -split -bg -ibam accepted_hits_negStrand_2ndPair.bam -g mm9.size >| accepted_hits_negStrand_2ndPair.bedgraph"
- join the reads sharing the same strand
# This step is for fr-firststrand library (such as dUTP). which is
1+-,1-+,2++,2--
read1 mapped to ‘+’ strand indicates parental gene on ‘-‘ strand
read1 mapped to ‘-‘ strand indicates parental gene on ‘+’ strand
read2 mapped to ‘+’ strand indicates parental gene on ‘+’ strand
read2 mapped to ‘-‘ strand indicates parental gene on ‘-‘ strand
# input: bedgraph file from the same strand
# output: merged bedgraph: pos.bedgraph or neg.bedgraph
unionBedGraphs -i accepted_hits_posStrand_2ndPair.bedgraph accepted_hits_negStrand_1stPair.bedgraph |awk '{ print $1"\t"$2"\t"$3"\t"$4+$5 }' >|pos.bedgraph
unionBedGraphs -i accepted_hits_posStrand_1stPair.bedgraph accepted_hits_negStrand_2ndPair.bedgraph |awk '{ print $1"\t"$2"\t"$3"\t-"$4+$5 }' >|neg.bedgraph
- To check how reads were stranded for strand-specific RNA-seq data, you can run infer_experiment.py from RSeQC or visit BaRC SOP: SAM/BAM summarizing, processing and quality control(QC)
infer_experiment.py -r mm9.refseq.bed12 -i accepted_hits.bam
- convert bedgraph to bigwig
# get rid of header lines of mm9.size: the header line with "chrom size" is removed
# input: mm9.size: length of each chromosome
# output: mm9.size_noHeader
tail --line=+2 mm9.size > mm9.size_noHeader
# convert bedgraph to bigwig
# input: bedgraph file: neg.bedgraph or pos.bedgraph
# mm9.size_noHeader: length of each chromosome
# *output: bigwig format: neg.bw or pos.bw
# neg.bw or pos.bw can be visualized with IGV/UCSC genome browser
bsub bedGraphToBigWig neg.bedgraph mm9.size_noHeader neg.bw
bsub bedGraphToBigWig pos.bedgraph mm9.size_noHeader pos.bw
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