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Example use case creating an ``PairwiseAlignment`` instance as per the tutorial:
```pycon
>>> from Bio import Align
>>> aligner = Align.PairwiseAligner()
>>> seq1 = "GAACT"
>>> seq2 = "GAT"
>>…
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### Description of the bug
Hi all,
I've downloaded references from [Gencode]( https://www.gencodegenes.org/human/) (i.e. genome, transcript, annotation) and used nf-core/rnaseq with `--aligner sta…
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When I use HiC to help assemble genome, I run the following code:
/ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/juicer/scripts/juicer.sh -t 30 -g RT -z refere…
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I recently processed Hi-C data provided by a colleague of mine, who performed the alignment steps. I then used `hicBuildMatrix` in conjunction with `findRestSites` to produce a contact matrix with fra…
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I know this problem was reported previously. I checked all the answers and I can see there are many reasons for this. In my case, I have a 'high number of mappings discarded because of alignment score…
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Hi, there. Thank you for developing such a useful tool. I have a question about the quantify reads in alignment-based mode.In my bam file, how many times does samlon count the identical read A00399:21…
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When I run the following command:
```bash
export NXF_OPTS='-Xms1g -Xmx4g'
nextflow run -r 1.0.0 nf-core/scrnaseq\
--reads 'data/H204SC19123229/raw_data/*/*_R{{1,2}}_001.fastq.gz'\
…
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### Description of the bug
-[nf-core/rnaseq] Pipeline completed with errors-
Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (GRCh38.primary_assembly.genome.fa)'
…
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## Description of the bug
Passing an additional FASTA to add to an annotation (e.g. ERCC spike-ins) results in their "type" in the resulting GTF to be set as "gene_biotype". This is an issue when u…
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### Description of the bug
Hi,
I run the following command:
```
module load Singularity/3.1.1
nextflow run nf-core/rnaseq --input $1 -profile singularity --fasta ~/22.genome/susScr11_xy/Sus_scr…