...-i <BAM> -fq <FQ>Options: -fq2 FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name is creating paired FASTQ. -tags Create FASTQ based on the ma...
...** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:...
...eria: (i) reads with ≥10 % unidentified nucleotides (N); (ii) reads forwhich more than 50 % of the read length had a Phred quality value ≤10; (iii) reads with the adapter. The cleaned data were aligned on to the reference genome using BWA-MEM (0.7.10-r789) with default parameters[1], SAMTO...
...g trouble debugging this error, first read the best practices
tutorial for helpful tips that address many common problems
http://www.circos.ca/documentation/tutorials/reference/best_practices
The debugging facility is helpful to figure out what's happening under the
hood
...
...码成一个字母记录序列信息：
数据来源：https://www.bioinformatics.org/sms/iupac.html
IUPAC nucleotide codeBaseAAdenineCCytosineGGuanineT (or U)Thymine (or Uracil)RA or GYC or TSG or CWA or TKG or TMA or CBC or G or TDA or G or THA or C or TVA or C or GNany base. or -gap
这里是...
...是序列末尾的READ1 flag和READ2 flag，flag有3类：
1：Only READ1 is set.
2：Only READ2 is set.
O：Either both READ1 and READ2 are set；or neither is set.
对于PE测序reads，同时指定-1 R1.fq-2 R2.fq-s singleton.fq 时，samtools会将flag1和flag2配对的序列分别输出...
...unction (classes, fdef, mtable) :
unable to find an inherited method for function ‘dotplot’ for signature ‘"NULL"’
Calls: dotplot -> <Anonymous>
查了下需要升级R包：clusterProfiler等等
但是升级不成功：说magick安装不上，这里报错：
Error: pac...
error pulling image configuration: download failed after attempts=6: tls: failed to verify certificate: x509: certificate is valid for *.bjfu.edu.cn, bjfu.edu.cn, not production.cloudflare.docker.com