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sanger-tol / genomeassembly

Implementation of ToL genome assembly workflows
https://pipelines.tol.sanger.ac.uk/genomeassembly
MIT License
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genomeassembly usage #34

Closed abdo3a closed 7 months ago

abdo3a commented 7 months ago

Hi There, I'm so happy that this pipeline has been released, I was looking forward to using it. But while trying it on my data, I realized that the HiC dataset needs to be in .CRAM but I have it as paired .FASTQ (F and R).

yumisims commented 7 months ago

you could convert your fastq file to cram using samtools import, eg.

samtools import -@8 -r ID:${prefix} -r CN:${hic_kit} -r PU:${prefix} -r SM:${sample_name} ${r1}.fastq.gz ${r2}.fastq.gz -o ${prefix}.cram
samtool index ${prefix}.cram
abdo3a commented 7 months ago

Thanks so much, @yumisims, i follow your suggestions, and the pipeline works handsomely on the yeast sequencing test data.