使用final.bam文件运行velocyto

[Xixu551]

我想要运行velocyto，而华大仅返回了fastq文件和final.bam文件(约60GB），当我运行如下命令：

velocyto run --bcfile /home/chenzhizhuo/Data/keloid/ActK6/barcodes.tsv.gz --outputfolder ./velocyte/ActK6 /home/chenzhizhuo/Data/keloid/ActK6/final.bam /home/chenzhizhuo/refdata-gex-GRCh38-2020-A/genes/genes.gtf

出现了如下报错：

[E::idx_find_and_load] Could not retrieve index file for '/home/chenzhizhuo/Data/keloid/ActK6/final.bam'

[lishuangshuang0616]

I'm not sure about the contents of the returned final.bam file. Judging from your error report, you need to build an index for final.bam and use samtools index. If your final.bam is not sorted, you have to use samtools sort to sort.

[Xixu551]

I'm not sure about the contents of the returned final.bam file. Judging from your error report, you need to build an index for final.bam and use samtools index. If your final.bam is not sorted, you have to use samtools sort to sort.

Is there any arguments to let velocyto identify .bai file from 'samtools index'?

[lishuangshuang0616]

Sorry, only need samtools sort

[Xixu551]

Sorry, only need samtools sort

I notice that the RNA velocity matrix in output directory has the following structure: antisense.mtx.gz features.tsv.gz spliced.mtx.gz barcodes.tsv.gz spanning.mtx.gz unspliced.mtx.gz Is there any thing I can do to convert it to .loom files so that it can be compatible with Scvelo's or Velocyto's python implemention?

[yangyiling10]

我也有这个问题，请问您解决了吗