tk2/RetroSeq
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
Perl
Issues
- 2
- 9
Error when trying to run bedtools intersect
#18 opened by kutsukos - 2
- 0
Defaults in -call
#23 opened by MaximilianStammnitz - 9
Uninitalized value error post PE parsing
#4 opened by biobenkj - 0
Cant find BAM input file or BAM index file
#22 opened by zhutao1009 - 0
Cant find BAM input file or BAM index file
#21 opened by zhutao1009 - 1
hets option for the calling phase
#20 opened by Milad021 - 3
Running RetroSeq on heterozygous data
#11 opened by jacau - 0
- 1
Is RetroSeq still able to handle split reads?
#14 opened by pyrevo - 2
FATAL ERROR : Unrecognised symbol
#15 opened by Leelouh - 1
- 0
Discovery Phase
#16 opened by xuqiangzhang - 3
Separating .vcf's by individual on pooled call?
#12 opened by lokeyCEU - 0
$cfh or $currentTypeAnchorsFile?
#10 opened by kbrevs - 5
install and launch
#5 opened by EmmyDx - 2
Compatibility Checks for samtools
#9 opened by jfong1123 - 1
Installation and launch
#8 opened by jfong1123 - 1
retroseq.pl line 158.rence file
#6 opened by tito3000 - 4
Error while calling TEs from pooled samples
#1 opened by frl1 - 0
Filtering calls
#3 opened by ramaniak - 2
Coordinate system query
#2 opened by cbergman