Download sra file in r

You should contact the package authors for that. Tweet to rdrrHQ. GitHub issue tracker. Personal blog. What can we improve?

The page or its content looks wrong. I can't find what I'm looking for. I have a suggestion. Errors during downloads It is not unusual for users to get errors while downloading SRA data with prefetch, fasterq-dump, or hisat2, because many people are constantly downloading data and the servers can get overwhelmed.

Please see the NCBI SRA page Connection Timeouts Estimating space requirements fasterq-dump takes significantly more space than the old fastq-dump, as it requires temporary space in addition to the final output. As a rule of thumb, the fasterq-dump guide suggests getting the size of the accession using 'vdb-dump', then estimating 7x for the output and 6x for the temp files.

It is also recommended that the output file and temporary files be on different filesystems, as in the examples below. Downloading data from SRA You can download SRA fastq files using the fasterq-dump tool, which will download the fastq file into your current working directory by default.

Note: the old fastq-dump is being deprecated. For example, on Helix, the interactive data transfer system, you can download as in the example below. To download on Biowulf, don't run on the Biowulf login node ; use a batch job or interactive job instead. Submitting a single batch job 1. Create a script file similar to the one below. Asked 1 year, 3 months ago. Active 1 year, 2 months ago. Viewed 2k times.

I tried using this method: where i downloaded. Improve this question. Timur Shtatland 8, 2 2 gold badges 22 22 silver badges 31 31 bronze badges. 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. Improve this answer. 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.