WebMar 17, 2024 · Details featureCounts is a general-purpose read summarization function that can assign mapped reads from genomic DNA and RNA sequencing to genomic features or meta-features. The function takes as input a set of SAM or BAM files containing read mapping results. The files might be generated by align or subjunc or any suitable aligner. Webto get the output in bam, use: samtools view -b -f 4 file.bam > unmapped.bam. To get only the mapped reads use the parameter F, which works like -v of grep and skips the alignments for a specific flag. samtools view -b -F 4 file.bam > mapped.bam. From the manual; there are different int codes you can use with the parameter f, based on what you ...
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WebFeb 15, 2024 · SAM and BAM files contain the same information; SAM is human readable and BAM is in binary code and therefore has a smaller file size. Find the official … WebOct 29, 2013 · $ awk '$1="chr"$1 {print}' file.in chr1 34566 34765 chr2 45678 45789 chr3 34567 34799 chrX 67895 66900 chrY 34567 34890. In essence, you are redirecting value of "chr"$1 back to $1 regardless if there are spaces before column 1 or not and still print out the rest of the line. WebThis command is much faster than replacing the header with a BAM→SAM→BAM conversion. By default this command outputs the BAM or CRAM file to standard output (stdout), but for CRAM format files it has the option to perform an in-place edit, both reading and writing to the same file. smart farming days bohmte