samtools

file cd ~/referencemkdir -p index/hisat cd index/hisatwget -c ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/hg19.tar.gzwget -c ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/mm10.tar.gztar zxvf hg19.tar.gztar xvzf mm10.tar.gz-C: Use resumable upload to compare, sort, and index the fastq-format reads to obtain the sam file, and then use samtools to convert it to the bam file, and sorting (note the differences between N and P) (you can use pipelines

. [1] 3. compress the Sam file into the BAM format samtools view –bS aln-pe_reorder.sam –o aln-pe.bam Search for samtools help: Usage: samtools -B indicates that the output file is in the BAM file format.-s indicates that the input file is a BAM file by default. If the input file is a SAM file, you 'd better add this parameter; otherwise, an error is reporte

After several days of exploration and online data query, the gatk software is a little cautious. The following is a summary: 1. It is best to use the FASTA file to locate the data on the chromosome. You do not need to comment out the VCF file (GVF). However, if you use the VCF file, ensure the following conditions: 1) The number of VCF chromosome and FASTA chromosome must be consistent in sequence. 2) VCF sites must be sorted in ascending order. 3) The VCF base may have other symbols, such

[1] bedtools (HTTPS://GITHUB.COM/ARQ5X/BEDTOOLS2)Here is also Bedtools (HTTPS://GITHUB.COM/ARQ5X/BEDTOOLS2) Getfasta. It uses Erik ' s code under the hood.$ cat test.fa>chr1AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG$ cat test.bedchr1 5 10$ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out$ cat test.fa.out>chr1:5-10AAACCDocs:http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.htmlAnd it is wrapped in pybedtools as well:http://pythonhosted.org/pybedtools/autodocs/pybedtoo

I. Summary The experiment aims to understand the basic principles of CHIP-SEQ. By imitating the process of the literature "targeting super enhancer associated oncogenes in oesophageal squamous cell carcinoma", we learned to download data using NCBI and EBI databases, Familiar with the basic operation of Linux, and use the R language to draw, using Python or shell to write scripts for basic data processing, through the FASTQC, Bowtie, Macs, Samtools, R

Unique reads: There is only one match point on the reference groupMulti-mapping reads: There are multiple matching points on the reference groupHere is a result case for tophat:Reads: Input : 26140314 Mapped : 25159791 (96.2% of Input) of these: 10276914.1%) has multiple alignments (1832 has >)96.2% overall read mapping rate.The quantity of unique reads:25159791-1027691=The quantity of multi-mapping reads:1027691How many alignment did the 1,027,691 multi-m

I have been familiar with Linux and Windows, but I am still not very familiar with Mac. Today I have spent a lot of time on Mac. Homer is a program for analyzing DNA motif and needs to be installed before use. First, visit http://biowhat.ucsd.edu/homer/introduction/install.htmlto download an installation script configurehomer.pl. CD to the directory, and then Perl configurehomer. pl-install to install Of course, it has some dependency, so you need to download some dependency such as

variants for a, and for example, use:Discovar \READS=READS.BAM \out_head=assembly \regions=1:50000150000\Reference=genome.fastaThe complete set of variant calls for this region is given in the text file:Assembly.final.variantInput filesDiscovar requires a BAM file containing the raw reads from the sequencer. For variant calling it alsoRequires a matching reference FASTA file.BAM filesThe reads to assemble must is in a BAM file or files. The name of the BAM file is specified with theRequired arg

specification can found on Https://github.com/samtools/hts-specsThis is under continued development, please check the Hts-specs page for the most recent specificationA PDF of the v4.1 spec is http://samtools.github.io/hts-specs/VCFv4.1.pdfA PDF of the v4.2 spec is http://samtools.github.io/hts-specs/VCFv4.2.pdfVcftools Host A discussion list about the specification called Vcf-spec http://sourceforge.net/p/vcftools/mailman/REF:Http://blog.sina.com.cn/