Process 10X xenium data

Locate the transcript file from your Xenium output, most likely named as transcripts.csv.gz.

The first few lines may look like (from the public human breast cancer dataset)

"transcript_id","cell_id","overlaps_nucleus","feature_name","x_location","y_location","z_location","qv"
281474976710656,565,0,"SEC11C",4.395842,328.66647,12.019493,18.66248
281474976710657,540,0,"NegControlCodeword_0502",5.074415,236.96484,7.6085105,18.634956

We will collapse pixels from all z-planes to 2D, essentially using only x_location, y_location, and transcript_id. You may want to keep only transcript with quality score qv above certain threshold.

The following command assume your input is in inpath and you you want to store output to path. In some data the negative control proves are names "Blank-*", --dummy_genes BLANK\|NegCon will regard any transcript_id containing the substring "BLANK" or "NegCon" as control probes. You could provide a regex according to your data.

The script format_xenium.py can be found in misc/ in the FICTURE repository.

input=${inpath}/transcripts.csv.gz
output=${path}/filtered.matrix.${iden}.tsv
feature=${path}/feature.clean.${iden}.tsv.gz

python format_xenium.py --input ${input} --output ${output} --feature ${feature} --min_phred_score 15 --dummy_genes BLANK\|NegCon

sort -k2,2g ${output} | gzip -c > ${output}.gz
rm ${output}