Souforce distinguishes mother fetal derived cells

[guanghui-tan]

I now have a spatial transcriptome sequencing bam file with a file size of 58g. As well as VCF files of individual variations in fetuses, Souforce is now used to distinguish cells from maternal and fetal sources. My script is as follows： singularity exec Demuxafy.sif souporcell_pipeline.py \ -i sorted.bam\ -b BeadLocationsForR.csv \ -f ARS-UCD1.2_Btau5.0.1Y.fa \ -t 20\ -o /work/home/luo_funong/Tan_Guang-hui/mutai_qufen/out \ -k 2 \ --known_genotypes /work/home/luo_funong/Tan_Guang-hui/mutai_qufen/chrAll_QC_filter.vcf \ --known_genotypes_sample_names maternal fetal --ignore true

The location information in the bam file is shown in the following figure：

BeadLocationsForR.csv file

When I ran the above script, there were no error log files and it was running continuously, but there was no result file output.

I would like to ask what is going on here

[yangchao4]

你好，我想在也碰到了类似的问题，请问您有解决吗，可以邮件联系吗huw4065@163.com

[XiaolongYang-HZAU]

I encountered a similar issue. I'm using the same data type and the same BAM tags, but I couldn't find where the tag corresponding to the barcode is located. This might be an issue with HuaDa instead of SoupCell. I also raised an issue in SAW, hoping to get it resolved. If you've already solved it, I hope to receive a reply.