rajewsky-lab mirdeep2 issues

rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data

GNU General Public License v3.0

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issues

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Duplicate IDs in precurser and miRNA fasta files give duplicate IDs in result tables

#76 milag6 closed 3 years ago
1
sanity_check_mature_ref.pl Error: problem with hairpin.fa

#75 sdjebali closed 3 years ago
1
ARF output error

#74 Yatzutzu closed 3 years ago
1
GNU parallel

#73 leorippel closed 3 years ago
1
Empty arf file

#72 TaliRB closed 3 years ago
2
File mirdeep_runs/run_07_09_2020_t_11_03_47/output.mrd is empty

#71 crikkia closed 3 years ago
7
memory issues sam to arf

#70 leorippel closed 4 years ago
2
Set up issue templates

#69 mschilli87 opened 4 years ago
1
make_html.pl - reading of output.mrd file

#68 Pfaendner closed 4 years ago
1
Running quantifier.pl

#67 anadc71 closed 4 years ago
1
Non-deterministic behaviour of miRDeep2

#66 Pfaendner closed 1 year ago
3
Deterministic miRDeep2_core_algorithm.pl

#65 Pfaendner opened 4 years ago
4
paired-end reads analysis

#64 sridewi1 closed 4 years ago
5
replacement of U with T in reference miRNA.fasta

#63 shannjiang closed 4 years ago
2
miRNAseq read length in mirdeep2

#62 shannjiang closed 4 years ago
2
miRDeep2 didn't generate output when species supplied by option -t is not in the allowed ucsc species list

#61 Jomagrax closed 4 years ago
28
fasta format

#60 Juliix closed 4 years ago
1
mapper.pl and bowtie option

#59 Juliix closed 4 years ago
3
Illegal division by zero error raised by mapper.pl when no reads could be mapped

#58 VenithaB closed 4 years ago
4
Issue running miRDeep2.pl with .mrd output from quantifier.pl

#57 plAnneting closed 4 years ago
6
mapper.pl not recognizing .ebwtl index files produced by bowtie 1.1.1

#56 VenithaB closed 4 years ago
4
It didn't generate any output files

#55 HaeWon-chung closed 4 years ago
7
got an error during manual installation of PDF-API2

#54 HaeWon-chung closed 4 years ago
9
plant miRNA predict

#53 huangl07 closed 4 years ago
3
Mapper block question

#52 JoseCorCab closed 4 years ago
1
mirdeep2 quantification questions

#51 Kennyluo4 closed 4 years ago
4
novel microRNA counts for each sample

#50 sridewi1 closed 4 years ago
2
miRNA normalization based on total reads includes multiple mapped reads

#49 andreasd closed 4 years ago
3
mirdeep2.pl:-g parameter

#48 zhengyzh closed 4 years ago
3
Detect synthetic miRNA via miRDeep2

#47 dinggens closed 4 years ago
1
Output bed files (press, mature and star) have the same coordinates

#46 LliliansCalvo closed 5 years ago
2
I got two different result when running miRDeep2 core algorithm twice

#45 pynie1 closed 5 years ago
4
Reads with mismatches are not mapped to the genome in the initial mapping by the mapper.pl

#44 evnovaes closed 5 years ago
9
No file mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.fa_stack found

#43 Yashrajsinh-Jadeja closed 5 years ago
5
Quantifier.pl maps zero mature sequences

#42 EPunzi closed 5 years ago
5
Can't locate Compress/Zlib.pm in @INC

#41 dansapozhnikov closed 5 years ago
17
miRDeep2.pl and mapper.pl input for novel species - one sample or all samples?

#40 dansapozhnikov closed 5 years ago
1
how to da data processing

#39 leiwaaping closed 5 years ago
2
miRDeep2 does not generate result.html

#38 sridewi1 closed 5 years ago
8
All candidates discarted "because the structure is inconsistent with Dicer processing"

#37 weedcentipede closed 5 years ago
1
Illegal left brace in line 2680

#36 weedcentipede closed 5 years ago
4
error in install.pl

#35 mahaamhamid closed 5 years ago
4
quantifier.pl -w error: "Mature mapping file hairpin_sfr.fa.dummy_mapped.bwt not found"

#34 hmontenegro closed 5 years ago
6
Read counts of quantifier module versus known miRNA detected by miRDeep2 module

#33 Nourolah closed 5 years ago
4
Estimated false positive number is greater than the number of reported novel miRNA precursors

#32 dudemain closed 5 years ago
12
Unique novel miRNA identifier

#31 Nourolah closed 5 years ago
4
species not at UCSC

#30 biopig closed 5 years ago
9
bin/env/perl -W Permission denied - Already solved; would like to share only!

#29 Nourolah closed 5 years ago
0
[RFC] Gracefully handle zero mapped reads

#28 mschilli87 closed 5 years ago
3
Uninformative error for zero-mappings.

#27 mschilli87 closed 5 years ago
4

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