I wonder if there is a way to get the file size from the NCBI server before downloading it. Also, I want to verify if the download of a BAM file was done properly by assessing that the file size is the same.
I used this command:
sam-dump SRR2937435 | samtools view -bS - > SRR2937435.bam
Is there a command that I could type to know this?
Depending on OS/storage the same file may show up with different sizes. Look at the number of reads SRA says this sample has and then compare your local copy.
You can browse and locate SRA files by using the ftp site at NCBI: ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/ That should allow you to gauge the size prior to download.
That's cool! I found that the .sra is 11.1GB but it does tell me what could be the BAM or SAM file. If I understand, there is not a way to verify this...
It's saying that there is a MD5 error...
That's from EBI-ENA. Is there a way that I can download the BAM file from the SRA file with Aspera?
By "new" I can only say that the article was published this year. But the sequences are there since a long time!
Grab the sra file directly from SRA here and then dump the fastq locally. See what you get.
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