10x_bam_to_fastq_seqnames:R1,R3,I1,R2 Read groups If the BAM file contains '@RG' headers and tags to indicate the source of each read, separate FASTQs will be created for each read group present in the BAM file. Known Issues
Bamt2fastq conversion has an non intuitive behavior: when reads are paired: it creates a temporary fast.gz which is actually a fastq uncompressed with both reads and then creates 2 fastq.gz with R1 and R2 separated when reads are single: it creates correctly a fastq.gz khourhin mentioned t...
BWA was used to map sequencing reads to the reference human genome (hg38). Bam files were further analyzed with CRISPResso2 version 2.0.3158. An input gene list with 20 bp gRNA sequence (no PAM included) for each target and chromosome coordinates for a 41 bp mapping region with the ...
bwa mem-M-t16Staphylococcus_aureus.fastaERR043371_1.fastqERR043371_2.fastq>output.sam sam文件转换为bam 代码语言:javascript 复制 samtools view-Soutput.sam-Obam-o output.bam bam文件排序 代码语言:javascript 复制 samtools sort output.bam-@16-Obam-o output.sorted.bam 计算覆盖度 代码语言:javascript...
out of the box. However, many conversions require external tools. This is why we recommend to use acondaenvironment. In particular, most external tools are available on thebiocondachannel. For instance if you want to convert a SAM file to a BAM file you would need to installsamtoolsas ...
[1] "Converting sam file to sorted bam file on XXX.cluster.XXX.de : /scratch/boulanger/tmp/RtmpOSr6zM/GJFV9_Drosophila_SMF_23s002742-1-1_Li_lane1NMB5_1_sequence.txt.gz_val_1.fq.gz3d3886479912f7.fastq3d3886286e5f1b.sam" [1] "Error on XXX.cluster.XXX.de processing sample /scratch...
Similarly, the mason2fq command converts mason2 simulated SAM to FASTQ. Command mapeval evaluates mapped SAM/PAF. Here is example output: The splice2bed allows to convert paf to BED, and then use bedtools coverage which accepts BAM/BED/GFF/VCF file(s) Hope any of this can help you. ...