2. `-R /data/bio-wenzl/hg38_old/hg38.fa`: 指定参考基因组的路径,这里是hg38版本的人类基因组FASTA文件。 3. `-I /data/bio-wenzl/hg38_old/11-y-PBMC.sorted.markdup.bam`: 指定输入的BAM文件路径,该文件是经过排序和去重处理的比对结果,包含了样本11-y-PBMC的测序读段 4. `-O /data/bio-...
引文格式: Shifu Chen. (2023). Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp.iMeta,https://doi.org/10.1002/imt2.107 作者简介 陈实富(第一/通讯作者) ● 中科院博士,海普洛斯创始人兼首席技术官,中科院深圳先进技术研究院客座研究员。 ● 2019年深圳市青年科技...
${i}_combined_R2.fastq.gz & done 3. 比对 #for i inls *_out_R1.fastq.gz; do i=${i/_out_R1.fastq.gz/}; nohup hisat2 -p 8 --dta -x /path/to/file/hg19/genome -1 ${i}_out_R1.fastq.gz -2 ${i}_out_R2.fastq.gz -S ${i}.sam & done 4. 排序 for i inls *....
exit 1 fi less "$1" | awk '{if(NR%4==0) printf("%s ", $0);}' | od -A n -t u1 -v | awk ' BEGIN { valid = 1; min_len = 1000000; max_len = 0; } { len = NF; if (len < min_len) min_len = len; if (len > max_len) max_len = len; for (i = ...
i=str(i.seq) total_reads+=1total_bases+=len(i) print("total_reads:"+str(total_reads)) print("total_bases:"+str(total_bases)) (base) [b20223040323@admin1 test]$python test.py SRR1770413_1.fastq SRR1770413_2.fastqtotal_reads:6total_bases:1806 ...
i=i+4 当二代测序的原始数据拿到手之后,第一步要做的就是看一看原始reads的质量。常用的工具就是FASTQC。 FASTQC的官网: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FASTQC的下载地址: http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc 在linux上的安装 $wget http:/...
fastq-dump --gzip --split-3 /home/u3893/rna_seq_AKAP95/sra/SRR3589962 -O /home/u3893/rna_seq_AKAP95/data/rna_seq 也可以循环执行命令,但时间较长foriin`seq56 62`;dofastq-dump --gzip --split-3 /home/u3893/rna_seq_AKAP95/sra/SRR35899$i-O /home/u3893/rna_seq_AKAP95/data/rna...
Low complexity filter is disabled by default, and you can enable it by -y or --low_complexity_filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]). For example:...
fastq wrapper persisted queue on disk to save some memory. Latest version: 0.1.9, last published: 3 years ago. Start using disk-fastq in your project by running `npm i disk-fastq`. There are no other projects in the npm registry using disk-fastq.
less$1|head -n1000|awk'{if(NR%4==0) printf("%s",$0);}'\|od -A n -t u1 -v\|awk'BEGIN{min=100;max=0;} \{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END \{if(max<=126 && min<59) print "Phred33"; \else if(max>73 && min>=64) pri...