lapa

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Hi, I am using lapa for the DRS and cDNA ONT data. While it runs smoothly in DRS, in case of the cDNA reads, it throws an error at the...

nemitheasura

pyrange error "ValueError: all elements of `new_shape` must be non-negative"

11

Hi Mihammed, I got the following pyrange error: Traceback (most recent call last): File "/cluster/work/bewi/members/dondia/Anaconda3/envs/snakemake/bin/lapa", line 8, in sys.exit(cli_lapa()) File "/cluster/work/bewi/members/dondia/Anaconda3/envs/snakemake/lib/python3.9/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "/cluster/work/bewi/members/dondia/Anaconda3/envs/snakemake/lib/python3.9/site-packages/click/core.py",...

ArthurDondi

Refining transcript 3' and 5' ends with LAPA

3

Hi @MuhammedHasan I see that you have 'lapa.correction.Transcript' how would I be able to use it. To my understanding default LAPA deals with 'gene_id' how would I change the analysis...

MustafaElshani

AssertionError: Can only do stranded operations when both PyRanges contain strand info

5

I use LAPA on aligned pacbio data from minimap2 I got the following error: File "/usr/nzx-cluster/apps/lapa/python3.8.11/bin/lapa", line 8, in sys.exit(cli_lapa()) File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) File...

leli-li

It seems that `lapa_correct_talon` is looking for a column named ` samples ` in the TALON generates `read_annot` file. This column is not available, however sample names are in `dataset`...

MustafaElshani

If detected that the product of the sizes of df and gr_bam are over 2^31, will subset them both to avoid the overflow error. Will cause in a few lost...

leetaiyi

Value error need at least one array to concatenate

5

Hi, I am running LAPA with the command - lapa --alignment /data/salomonis-archive/FASTQs/Grimes/RNA/scRNASeq/10X-Genomics/LGCHMC53-17GEX/PacbioPBMC/PacbioPBMC/outs/possorted_genome_bam.bam --fasta hg38.fa --annotation hg38.gtf --chrom_sizes hg38.chrom_sizes --output_dir pbmc_pacbio_1 I am getting this error - a3-2020/lib/python3.8/site-packages/click/core.py", line 1066, in...

Priyankanator

Installation error

3

Hello, I am encountering problems installing lapa. Here is the error I am getting ``` #0 1.082 Collecting lapa #0 1.115 Downloading lapa-0.0.5-py3-none-any.whl (36 kB) #0 1.132 Requirement already satisfied:...

sagnikbanerjee15

Hi Muhammed, I'm trying to test lapa with RNAseq short reads. I'm using hisat2 for the mapping ( I built the hg38 with transcript index using the files suggested in...

emaxortiz