Bam file does not have umi tags

[shaaaarpy]

Hi I am using https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8869110 this data for my processing.

When i am using only the bam file, i get killed error in creating loom file part. But as suggested in the tutorial, i sorted it using samtools (i think this bam was already sorted) and start geeting the UMI error. OSError: The bam file does not contain cell and umi barcodes appropriatelly formatted. If you are runnin UMI-less data you should use the -U flag. -U flag is also not working and giving the same error again Can you please suggest how to proceed.

Thank you

[HoxB8]

Hi I've been trying to trouble shoot a similar problem when trying to run velocyto on the bamfiles. I try to use samtool to sort as recommended

samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam

AND THEN I RAN VELOCYTO

velocyto run -b filtered_feature_bc_matrix/barcodes.tsv -o ./ -m ../../repeat_msk.gtf cellsorted_possorted_genome_bam.bam ../../gencode.vM24.annotation.gtf

Output...it tries to read 5000 lines 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4991 of the bam file 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4992 of the bam file 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4993 of the bam file 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4994 of the bam file 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4995 of the bam file 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4996 of the bam file 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4997 of the bam file 2020-03-28 08:36:05,941 - WARNING - Not found cell and umi barcode in entry 4998 of the bam file 2020-03-28 08:36:05,942 - WARNING - Not found cell and umi barcode in entry 4999 of the bam file 2020-03-28 08:36:05,942 - WARNING - Not found cell and umi barcode in entry 5000 of the bam file Traceback (most recent call last): File "/wynton/home/werblab/liusuy/.local/bin/velocyto", line 11, in load_entry_point('velocyto==0.17.17', 'console_scripts', 'velocyto')() File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/click/core.py", line 829, in call return self.main(*args, **kwargs) File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/velocyto/commands/run.py", line 116, in run samtools_memory=samtools_memory, dump=dump, loom_numeric_dtype=dtype, verbose=verbose, additional_ca=additional_ca) File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/velocyto/commands/_run.py", line 159, in _run exincounter.peek(bamfile[0]) File "/wynton/home/werblab/liusuy/.local/lib/python3.6/site-packages/velocyto/counter.py", line 158, in peek raise IOError("The bam file does not contain cell and umi barcodes appropriatelly formatted. If you are runnin UMI-less data you should use the -U flag.") OSError: The bam file does not contain cell and umi barcodes appropriatelly formatted. If you are runnin UMI-less data you should use the -U flag. [liusuy@qb3-dev3 outs]$ velocyto run -b filtered_feature_bc_matrix/barcodes.tsv -o ./ -m ../../repeat_msk.gtf cellsorted_possorted_timed out waiting for input: auto-logouttion.gtf

I much appreciate any insights.

[wupeng2]

Hi shaaaarpy, I have the same problem when i run samtools sort. OSError: The bam file does not contain cell and umi barcodes appropriatelly formatted. If you are runnin UMI-less data you do you fix it ,and how? thanks

[ZJ-zuojing]

@shaaaarpy @wupeng2 Hi, I also have the same problem, do you slove it? look forward to your reply . thanks!