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Commit 79a51d31 authored by Matteo Barcella's avatar Matteo Barcella
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Update README.md

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...@@ -20,14 +20,11 @@ Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17 ...@@ -20,14 +20,11 @@ Fastq files were aligned with [BWA aligner](https://github.com/lh3/bwa) (v0.7.17
- gatk BaseRecalibrator --input SampleID.dedup_reads_mouse_recal.bam --reference $genome --known-sites $vreference --output SampleID_post_recal_data_mouse.table - gatk BaseRecalibrator --input SampleID.dedup_reads_mouse_recal.bam --reference $genome --known-sites $vreference --output SampleID_post_recal_data_mouse.table
``` ```
## Disambiguation ## ## Disambiguation ##
We perform alignment using both human and mouse reference genomes in order to perform reads disambiguation using [disambiguate](https://pubmed.ncbi.nlm.nih.gov/27990269/) and discard reads from human mapping that belong to mouse cells. We perform alignment using both human and mouse reference genomes in order to perform reads disambiguation using [disambiguate](https://pubmed.ncbi.nlm.nih.gov/27990269/) and discard reads from human mapping that belong to mouse cells.
<details><summary>Code</summary> `python disambiguate.py -a bwa -s SampleID 02-Alignment_human/SampleID.dedup_reads_rehead_recal.bam 02-Alignment_mouse/SampleID.dedup_reads_mouse_recal.bam`
`python disambiguate.py -a bwa -s Sample_10_395_3 02-Alignment_human/SampleID.dedup_reads_rehead_recal.bam 02-Alignment_mouse/SampleID.dedup_reads_mouse_recal.bam`
</details>
# Variant calling # # Variant calling #
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