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. Multi-Gem Group BAM files created by Cell Ranger 1.2 and earlier do...
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...
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 ...
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 ...
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. ...
Hints for sam/bam --- * To run fast on multiple CPUs, and get a correct header at the top, this may be the least-awkward way. First, make a header (perhaps by using CreateSequenceDictionary). Then, concatenate the output of a command like this:: parallel-fastq ...