通过bedtools中的bamtofastq 能够将文件转成fastq bedtools可以通过conda安装,可以参考我往期的教程:https://www.jianshu.com/p/e82a8d799b13 1、软件的使用和说明 bedtools bamtofastq [OPTIONS] -i<BAM>-fq<FASTQ> 软件说明 2、实例 这里以常见的双端测序文件为例,通过的bam是按照染色体位置排序的,这里需要...
bamtofastqis a tool for converting 10x Genomics BAM files back into FASTQ files that can be used as inputs to re-run analysis. The FASTQs will be output into a directory structure identical to themkfastqorbcl2fastqtools, so they are ready to input into the next pipeline (e.g.cellrange...
Convert 10x BAM files to the original FASTQs compatible with 10x pipelines - 10XGenomics/bamtofastq
Hi SRA team, I have a question of how to check the integrity of the BAM or FASTQ files. The .sra.vdbcache files were downloaded using prefetch and validated using vdb-validate. But how can I check whether the extraction of BAM or FASTQ files from .vdbcache was complete and did not ...
If you need unmappedR1.fastq (containing both paired and unpaired R1 unmapped reads) and unmappedR2.fastq ( containing both paired and unpaired R2 unmapped reads). Use samtools -f 4 to extract all unmapped reads : 1 2 samtools view -b -f 4file.bam > file_unmapped.bam ...
If you need unmappedR1.fastq (containing both paired and unpaired R1 unmapped reads) and unmappedR2.fastq ( containing both paired and unpaired R2 unmapped reads). Use samtools -f 4 to extract all unmapped reads : 1 2 samtools view -b -f 4file.bam > file_unmapped.bam ...
能够将文件转成fastq bedtools可以通过conda安装，可以参考我往期的教程： https://www.jianshu.com/p/e82a8d799b13 这里以常见的双端测序文件为例，通过的bam是按照染色体位置排序的，这里需要先通过samtools sort -n将bam文件改成安装reads名排序，其次通过bedtools bamtofastq将bam转成fastq。
nextflow run nf-core/bamtofastq \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR> Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can ...
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too - divonlan/genozip
Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling. - mehdimerbah/WES