TreesLab NCLscan issues

TreesLab / NCLscan

We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.

MIT License

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issues

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removed debug print from output

#32 selkovjr opened 7 months ago
2
There are no main datasets assigned.

#31 kopardev opened 1 year ago
1
Using too much RAM (memory)

#30 kopardev opened 1 year ago
1
can not generate the CircRNA with NCLscan version

#29 JianGuoZhou3 opened 1 year ago
3
Failed to HRA000524 dataset (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000524)

#28 JianGuoZhou3 opened 2 years ago
7
NCLscan CAN NOT work anymore, it belongs to the License that expired on 9 Aug 2021?

#27 JianGuoZhou3 closed 2 years ago
0
No common_IDs between {prefix}.JS.seq_1 and {prefix}.JS.seq_2

#26 selkovjr opened 2 years ago
0
some samples can't get any result by NCLscan

#25 JianGuoZhou3 closed 3 years ago
12
Error: Cannot open input sequence files. output/clean.main.unmapped_1.fastq output/clean.main.unmapped_2.fastq

#24 JianGuoZhou3 closed 3 years ago
18
Can we choose another tools?

#23 JianGuoZhou3 closed 3 years ago
0
novoalign fails to create index

#22 BarryDigby closed 4 years ago
5
NCLscan finishes with an empty result file

#21 HosseinAsghari opened 4 years ago
5
NCLscan and unpaired read data?

#20 wolfgangrumpf opened 5 years ago
3
Alternative to Novalign?

#19 wolfgangrumpf opened 5 years ago
0
fix a bug that missed by g++ of version <= 6

#18 chiangtw closed 5 years ago
1
compilation error with GCC8

#17 peutch closed 5 years ago
2
bugfix: get_gene_name.py: fix default value for non-annotated junc-sites

#16 chiangtw closed 5 years ago
0
NCLscan error: "does not appear to be a valid novoindex. Code 9"

#15 Swadha22 closed 5 years ago
3
fix the re pattern to fit the newer bedtools

#14 chiangtw closed 6 years ago
0
fix duplicate sequence name issue

#13 chiangtw closed 6 years ago
0
Not reading files from the dirctory

#12 archu87 closed 5 years ago
15
error : Format Error! Z3 is not available!

#11 misik closed 5 years ago
1
Reference index

#10 misik closed 7 years ago
1
Is free version of novoalign not adequate to NCLscan ?

#9 tyaoi closed 5 years ago
9
Error in NCLScan Run

#8 onkarnath89 closed 5 years ago
0
JSFilter Segmentation fault

#7 arthuryxt closed 5 years ago
5
Is it possible to retrieve the pseudo-references??

#6 Aufiero closed 8 years ago
1
Where are Total number of all support reads, Total number of junc-reads, Total number of span-reads in .result file

#5 NitinMandloi closed 5 years ago
19
How the last 2 parameters in configuration file: config.txt affect results and when the updated version will probably be released?

#4 linatbeishan closed 8 years ago
3
why look for tools in the current working directory?

#3 brianjohnhaas closed 8 years ago
1
Where's the source code?

#2 brianjohnhaas closed 8 years ago
3
Issues and question NCLscan_v1.4

#1 vincenthahaut closed 8 years ago
11