gpertea stringtie issues

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

MIT License

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issues

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--merge disregards -G option?

#350 NoahHenrikKleinschmidt closed 2 years ago
2
Expected ballgown output when not using '-e'

#349 gabepen closed 2 years ago
3
Mangled new lines in coverage gtf file

#348 OXB-DC closed 2 years ago
4
running with point feature file

#347 Amhaslam closed 2 years ago
2
Can '--mix' option integrate CAGE data and Iso-seq?

#346 Jung19911124 opened 2 years ago
0
Malformed t_data.ctab file

#345 adc0032 closed 3 years ago
0
Gene id duplication caused by prepDE3.py

#344 jgreen51515 opened 3 years ago
0
Merge BAM files from biological replicates or not

#343 biozzq closed 2 years ago
1
dictionary optimization

#342 yollct closed 3 years ago
1
Suggestion for improving on annotation transcript start and end positions

#341 shernadi opened 3 years ago
0
question about gene_abund.tab, the GENEID's number and order are not equal

#340 lielab opened 3 years ago
0
How to integrate point-feature option in the standard workflow ?

#339 camelest opened 3 years ago
1
invalid feature coordinates from long read 'collapsed' assembly

#338 noncodo opened 3 years ago
3
prepDE.py error: could not locate transcript

#337 huangwb8 closed 2 years ago
5
Using the new --mix option for short and long-read data

#336 niradsp opened 3 years ago
0
Merge option gives different transcript numbers depending upon how the GTFs are provides

#335 sanyalab closed 3 years ago
2
Must the GTF file used by stringtie be the same as the GTF file used by aligner?

#334 ZHIDIHUAYUAN opened 3 years ago
0
Can stringtie add UTR to guided transcripts?

#333 krabapple opened 3 years ago
3
How can Stringtie decide the strand of a transcript assembled by a standard RNA library?

#332 ZHIDIHUAYUAN closed 3 years ago
3
Issue running prepDE.py

#331 G-Molano-LA opened 3 years ago
0
-ptf option - recommended input & implementation details?

#330 SamBryce-Smith opened 3 years ago
0
Questions concerning implementation of -i option

#329 tonyaseverson opened 3 years ago
0
duplication of gene level data from prepde

#328 jcohn42 opened 3 years ago
1
segmentation fault with long read data [ stringtie v2.1.4 ]

#327 daniel-spies closed 3 years ago
2
Unable to load stringtie in Linux

#326 kchen96 closed 3 years ago
1
Question about long reads splice sites correction

#325 youyupei opened 3 years ago
0
Issues with -M parameter

#324 bvaldebenitom opened 3 years ago
0
Question to StrigTie and the use of strand-specific data

#323 cc-prolix opened 3 years ago
0
gtf assembled using stringtie has lines missing strand info

#322 linzhangTuesday opened 3 years ago
2
How do you convert MSTRG.number to Gene name or Gene symbol?

#321 ghost opened 3 years ago
2
GVec error

#320 RAWWiberg closed 6 months ago
16
output files shorter than others

#319 gianfilippo closed 3 years ago
4
GVec error: invalid index: 18

#318 gianfilippo closed 3 years ago
4
AttributeError: 'NoneType' object has no attribute 'group'

#317 daniellembecker closed 3 years ago
7
de-novo transcript assembly using genome-guided bam

#316 ARW-UBT opened 3 years ago
1
STAR -> StringTie run giving very small number of novel exons/introns/loci (<1.0% of total)

#314 JenW1984 opened 3 years ago
2
Gene IDs after updated prepDE.py

#313 asumann opened 3 years ago
1
What is the "-m" option doing

#312 ytcheung opened 3 years ago
2
my sample consume a lot of memory

#311 tlz4320 opened 3 years ago
1
Stringtie stopped writing to tmp folder

#310 wenweixiong opened 4 years ago
2
Negative coverage values (version 2.1.3b)

#309 junghoon-shin opened 4 years ago
0
Error at GBitVec: index 31 out of bounds (size 8) during stringtie --merge

#308 mirahan opened 4 years ago
0
long read + RNAseq

#307 jdmontenegro opened 4 years ago
9
How to get feature counts using prepDE.py?

#306 mathavanpu opened 4 years ago
0
Why stringtie2.1.4 is not better than stringtie1.3.5 ?

#305 jinghui1012 opened 4 years ago
0
still have an issue with MSTRG in place of transcriptname and geneID after using gffcompare annotation mode

#304 laurentierney opened 4 years ago
0
Tuning parameters for long-read alignment prior to stringtie2

#303 shnmunk opened 4 years ago
0
Error running prepDE.py

#302 venuraherath closed 4 years ago
0
Stringtie 2.1.4: Error running prepDE.py

#301 venuraherath closed 4 years ago
1
Error: Getting the input alignment file is not sorted! even though file is sorted

#300 venuraherath closed 4 years ago
7

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