Adipose sample is missing data file

[goepp]

Hi, I noticed that sample GSM3711788 is missing the filter, metrics, and mx_out folders.

[goepp]

Hi, After closer examination, here is the list of samples which I have found to be missing data:

• no metadata.json: lung/GSM4213830
• no observation.json: blood/CRX102288 blood/CRX118014
• no filter folder: lung/GSM4339774 lung/GSM3773109 lung/GSM4339771 lung/GSM3773122 lung/GSM4339770 adipose/GSM3711788 tonsil/GSM5051493 tonsil/GSM5051493 tonsil/GSM5051496 rectum/GSM3576396 kidney/GSM4145206 kidney/GSM4145205 blood/GSM1676569 blood/GSM2560246 blood/GSM2560247 blood/GSM2560249 muscle/GSM4272893 muscle/GSM4272894 pancreas/all
• no mx_out folder: lung/GSM3773117 lung/GSM3773112
• no data at all: kidney/SRX3445570 kidney/SRX3445568 kidney/SRX3445567 kidney/SRX3445568 ileum/GSM3576431

In addition, there seems to be an error in the sample adipose/GSM3711758, as matrix.mtx.gzhas 3790 rows while barcodes.txt.gzhas only 2802 rows.

Hope this helps.

[sbooeshaghi]

Thank you! This is very helpful. We will investigate and report back.

[sbooeshaghi]

GSM4213830 done

I had to remove the CRX accessions since I was having trouble downloading the reads

GSM4339774 done GSM3773109 removed GSM4339771 done GSM3773122 removed GSM4339770 done GSM3711788 done GSM5051493 done GSM5051493 done GSM5051496 done GSM3576396 done GSM4145206 done GSM4145205 removed GSM1676569 removed GSM2560246 removed GSM2560247 removed GSM2560249 removed GSM4272893 done GSM4272894 removed GSM3773117 removed GSM3773112 removed

pancreas done SRX3445570 done SRX3445568 done SRX3445567 done SRX3445568 done GSM3576431 done GSM3711758

all anndata objects have been added in their respective folders (*/mx_out/adata.h5ad.gz).