WebSep 22, 2015 · If you're using Tophat2 then, by default, multi-mapped reads are not reported. That means accepted_hits.bam contains only primary alignments with one … WebJan 7, 2014 · The flagstat results are as follows: 36332416 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 32959970 + 0 mapped (90.72%:nan%) 36332416 + 0 …
FlagStat – GATK
WebApr 4, 2016 · Using the the samtools flagstat option I queried my read alignments. An example: 3232117 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates... WebDecoding SAM flags. This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties. To decode a given SAM flag value, just enter the number in the field below. The encoded properties will be listed under Summary ... can r run on macbook
sequence alignment - How to count the number of mapped read …
Websamtools-flagstat The tool does a full pass through the BAM/SAM/CRAM format input file and it calculates and returns statistics counts for each of 13 categories based on bit flags in the FLAG field. Each category is represented in the output as “#PASS + #FAIL”, followed by a short description of the category. Example: Input: WebBasic statistics shown by flagstat will be slightly different from those in the summary file generated by HISAT2 due to different "totals" that are used for comparisons. flagstat compares the number of alignments; HISAT2 compares the number of reads mapped. WebMar 3, 2024 · sorry to bother you. I would appreciate if you could help me interpret. As I mentioned I am interested in filtering out X/Y scaffolds from my assembly. I mapped my reads with minimap2, and I extracted the reads in a fasta file. With the following code samtools fasta -@ 48 -F 4 musXY.sam > musXY.sam.fasta can rso be given to dogs