Download sra data as bam file

It only takes a minute to sign up. Connect and share knowledge within a single location that is structured and easy to search. Normally, I would just use sam-dump , but the files are having issues that seem related to this issue. To this end, I created my own S3 bucket mm-mneuron and am now trying to copy from the SRA bucket to mine.

Here's what I try:. That is, it sounds like I can't access the SRA bucket. I've tested downloading and uploading to my bucket, so I know I have write permissions.

Not sure what else to try here. In this case, it means running the above within an EC2 instance colocated with the S3 bucket so, us-east-1 and having installed and configured SRA Toolkit to work from AWS as per this documentation. Unfortunately, the particular files I am concerned with are not currently accessible, but this should generically work in most situations. Sign up to join this community. The best answers are voted up and rise to the top.

You may either set the environment variables or you simply hard code the necessary locations in the configuration file. Create a variable representing the location we want to save our. Add these environment variables to your. Finally, convert the. Now we downloaded and converted a SRA file into. From here you can search these documents. Enter your search terms below.

You could first check with samtools that the bam file is at least readable with samtools: samtools view GSM You should also specify in your question how you tried to open the bam file in RStudio. What R functions did you use, what was the exact error message? Add a comment. Active Oldest Votes. Oh thanks so much, this looks to be very very helpful out of all the responses.

For samtools, I can't seem to download it which is odd I run on a Windows, is it possible to run it there? I'm gonna try again, maybe i didn't do the insatallation correctly, and again thanks for your help — ww22an. You're welcome. I don't think there is a Windows version for samtools. But you can install a Windows Subsystem for Linux WSL on your computer and it'll allow you to run linux commands even ssh and softwares on your Windows computer, so this might work for samtools.

Here are 2 tutorials to install the WSL : windowscentral. If none of that works, you can also try the online Galaxy to convert sam to bam : usegalaxy. Have you managed to read your bam files? If so, could you please accept the answer? Otherwise, tell me if you need more help! Sign up or log in Sign up using Google.