bergmanlab ngs_te_mapper issues

bergmanlab / ngs_te_mapper

Software for detecting transposable element insertions from next-generation sequencing data

BSD 3-Clause "New" or "Revised" License

14 stars 6 forks source link

issues

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add support for multithreading

#23 shunhuahan closed 5 years ago
0
rename insertion types in bed files

#22 cbergman closed 1 year ago
0
Remove legacy output and code

#21 cbergman closed 1 year ago
1
Change the TE database location

#20 cbergman closed 9 years ago
1
Recode R scripts to allow full paths for input files

#19 cbergman closed 9 years ago
1
Refactor example sequences

#18 cbergman closed 9 years ago
1
Add test to check that user generated output matches expected results

#17 cbergman closed 9 years ago
1
Change mapping engine from BLAT to BWA

#16 cbergman closed 9 years ago
1
Add ability to make predictions based on paired-end information

#15 cbergman closed 3 years ago
0
Add the ability to get insertions from sam files

#14 raquel-linheiro closed 10 years ago
3
recode fasta extraction from first psl result

#13 raquel-linheiro closed 9 years ago
1
include fastq to fasta conversion so system takes fastq as input

#12 raquel-linheiro closed 9 years ago
1
Add ability to identify if TEs in reference genome are present in sample

#11 cbergman closed 1 year ago
3
add citation file

#10 cbergman closed 10 years ago
1
add license

#9 cbergman closed 10 years ago
1
Add support to use blasr or bwa mem as mapping engine for PacBio reads

#8 cbergman closed 1 year ago
1
Do not keep reads that are ambigously mapping to start or end of the TE

#7 raquel-linheiro closed 9 years ago
2
Update system to allow multiple input files

#6 nelson42 closed 11 years ago
0
Add extensions to output files where necessary

#5 raquel-linheiro closed 11 years ago
0
Update readme to explain inputs and output of system

#4 raquel-linheiro closed 1 year ago
1
adapt TSD finding code to allow data from pooled individuals

#3 cbergman closed 1 year ago
0
update reference genome in example script to be UCSC compliant

#2 cbergman closed 11 years ago
1
update test data to have valid ENA identifiers

#1 cbergman closed 11 years ago
1