Websamtools view -D BC:barcodes.txt -o /data_folder/data.barcodes.bam /data_folder/data.bam Only keep reads with tag RG and read group grp2. This does almost the same than -r grp2 … http://quinlanlab.org/tutorials/samtools/samtools.html

Extract Reads From A Bam File That Fall Within A Given Region - Bi…

WebYou should use paired-end reads not the singleton reads. You can use following command from samtools to achieve it : samtools view -f2 -o If you want to understand... WebMar 10, 2024 · Explanations: -h in samtools view: export SAM file headers In awk, the substr function is used to keep header lines, and the rest two condition specify forward and reverse reads with the desired insert sizes, respectively Last but not least, samtools view -b is called to write the filtered reads into new a BAM file. tashes restaurant

extracting unmapped reads from BAM using Samtools?

WebTo get all of the reads in a single file, it is necessary to redirect the output of samtools fastq. The output file is suitable for use with bwa mem -p which understands interleaved files containing a mixture of paired and singleton reads. samtools fastq -0 … WebMaybe you can use 'samtolls view' to check detail of the bam file and then extract reads with keywords of your interested genes's name using custome comand line (I assume your reads have been... WebOct 12, 2015 · Extract reads from bam file by read name. While there are very fast and easy ways to extract reads from a bam file according to mapping location, extracting reads by … tashey enterprises