jaffa-project

Hi Alexey, Yes, the reference has become a little old now! If you would like to submit a github issue

Hi @cristoforo Sorry, I'm not 100% clear on what you are asking here. As Nadia mentioned, JAFFAL

A slow reply from me, but here is a relevant thread https://github.com/Oshlack/JAFFA/issues/102 On

Hello Belal, Sorry for the VERY slow reply. This sounds like a great application of fusion calling.

Hi Jyoti, Sorry for the slow reply. Would you mind posting this issue on JAFFA's github site,

Hi, JAFFAL developers! Thanks for making JAFFA available for long sequencing reads, which I believe

Hi Keisuke Kato, JAFFA has not been updated in bioconda for version 2 yet. Until we fix this, you can

Hello, When I am manually trying to install g++ -O3 -o bin/extract_seq_from_fasta ../src/

Hi, Replied at https://github.com/Oshlack/JAFFA/issues/57 Cheers, Nadia. On Wednesday, May 5, 2021 at

Hi, From this error message it appear that you don't have samtools installed. Once installed, you

Hi Sima, Yes this looks as expected. Unfortunately JAFFA is slow and not parallelized. The threads

Hi, This might be happening because you have another / conflicting groovy version installed to what

Hi, Did you change some of the variables in the .groovy file before you got this error? Did you put

Hi Wolfgang, No unfortunately JAFFA does not do this. Cheers, Nadia.

Hi all, I seem to have a problem in the Stage extract_fusion_sequences. I get this message: =========

Hi, I think that my reads are not getting mapped on the get-Umapped stage. Starting Pipeline at 2018-

Hi there I was trying to set up JAFFA and running it on the provided demo data. 1. The command I used

Sorry for so late reply. The fastq file is correct. My fastq file is as follows @9f64d3c8-12d3-4941-

I've figured out what the issue is. The resource file that you provide for hg38 (https://drive.

Hi Nadia, this time I have another issue with JAFFA version 1.08. See the follow output =============

Hi Nadia, I came across the same mistake: I am using java -1.8.0_65 and the output of sessionInfo()

The problem has been solved. I just forgot to specify the fastq files but not just the folder of

Hi Nadia, Another problem came. My files are fastq files with names of A1_1.fastq and A1_2.fastq. I

Hi, Did going back a version or two of JAFFA help you? Cheers, Nadia.

Hi Nina, I haven't been involved in the bioconda version of jaffa (it's very cool by the way

Hi, I just posted an answer in the previous thread, https://groups.google.com/forum/#!topic/jaffa-

Hi Alberto, It looks to me like the path to R has not been set in your tools.groovy file in the

Hi Romina, Unfortunately assembly can use a lot of memory. Do you know how much velvet is requesting

hell mam, You were right.I did my analysis with previous version of JAFFA and it ran. Thanks and

Hi Shikha, Since this is a different error that you're getting on a different dataset than the