Paired-end tags (PETs) are short, unique DNA sequences found at both 5′ and 3′ ends of a DNA fragment, meaning that they should be found only once in the genome, at that particular locus. From:Advances in Protein Molecular and Structural Biology Methods,2022 ...
折腾这么多都是白瞎,STAR就有输出没有别对上的pair-end reads的功能 参见:How To Filter Mapped Reads With Samtools I had the same issue but with Paired End Reads, and I solved using samtools and bamToFastq. You can find bamToFastq here:https://code.google.com/p/hydra-sv/ If you need u...
折腾这么多都是白瞎,STAR就有输出没有别对上的pair-end reads的功能 参见:How To Filter Mapped Reads With Samtools I had the same issue but with Paired End Reads, and I solved using samtools and bamToFastq. You can find bamToFastq here:https://code.google.com/p/hydra-sv/ If you need u...
SPAdes was a major improvement over previous assemblers like Velvet, but some of its components can be slow and it traditionally did not handle overlapping paired-end reads well. Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly ...
Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference. - GitHub - elzbth/jitterbug: Jitterbug is a bioinformatic software that
Targets of miRNA can be predicted based on Watson–Crick complementarity of the mRNA with the miRNA seed sequence (2–8 nucleotides starting from the 5 ´end. The longer sequence at the mRNA 3´UTR with matching nucleotides the more likely it is to be targeted19. We grouped the ...
40、inner mate distance for paired reads in a bam file 参考:https://www.biostars.org/p/106291/#106344 1、inner mate distance : the distance from the right most end of the left read to the left most end of the right read 2、the "insert size"=sequence between adapters (actually ...
(version 0.7.9 or higher) - BLAST to A-Bruijn graph package (available from https://github.com/COL-IU/RepGraph ) - Illumina or Illumina-like paired-end reads (whole-genome sequencing) - a reference genome sequence - as of v0.1.1, .medMAD file is generated AUTOMATICALLY from RepGraph ...
Read lines (fwd reads consitute the fwd clusters, rev reads the rev clusters) the reads' status can be "anchor": those that consitute the cluster, or "mate": are the anchors' mates, which map to a TE R cluster_pair_ID lib direction interval_start interval_end chrom status bam_line ...
the last column is a flag: PUTATIVE-SOM if less than 50% of the reads in that interval are not discordant (meaning it might be a somatic insertion in the tumor) and NON-SOM if notUSE CASE 3: leverage multiple samples for multi-sample calling...