How to download and transform BAM.1 files (Original format in SRA)

Question

[Wang]

Some Original format dataset have extention such as 'BAM.1'. How to download and transform those files with tools, such as fastq-dump

https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR1868750

Thank you for your attention!

[jkbonfield]

A bit late, and not an answer to fastq-dump (which tbh I just avoid like the plague!), but a trivial workaround.

This is an ERR file, so simply download it from EBI ENA and you'll get the original data without it being munged into SRA format. SRA often does funky things with read names, which can be detrimental to optical duplicate removal :(

https://www.ebi.ac.uk/ena/browser/view/ERR1868750?show=reads

Answer 1

[GenoMax]

Please search biostars before posting your questions (google works best). Many of your questions have been answered in past: Unable to convert single cell RNA Seq bam to fastq using cellranger's bamtofastq

[Wang]

Before asking, I searched Biostar forum and found no related questions, thank you for pointing out to use google.

[Wang]

My question including download multiple original format files, such as those files.

[GenoMax]

Not sure why there is a .1 at the end (which you can remove). You should be able to use the 10x utility to convert the BAM files to fastq.