tranfering sam file easy and fast way
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2.4 years ago
iamsmor • 0

Hi everyone

I was tried to align my fastq files by hisat2 but I could not able done because my computer has 4gb ram and I get error killed. So I performed process on my friend computer but now I should solve another problem that how I can transfer to files to my computer easy and fast way. we tried to upload onedrive and I had 12 sam files and it looks like take 2-3 days for uploading.

Do anyone can give me to any advice fro easier and faster way for uploading or transferring this files?

Thanks for any kind of help.

SAM RNA-seq hisat2 • 1.3k views
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Convert sam to bam using samtools view -o out.bam in.sam, that will compress data a lot. Beyond that, if internet connection is slow then that is what it is, no way to change that. Alternatively, put them onto an external drive and transfer from there.

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Be aware though that a computer with only 4GB RAM is not going to get you far. It will get stuck even on simpler tasks sometimes. Consider (if possible) to permanently upgrade RAM or switch to another machine.

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You could copy the files to an external drive and move them over. There are USB cables that allow you to move the data from one machine to other but you will need to purchase one.

If your computer only has 4G RAM then you are likely to run into some other block down the road when you start downstream analysis.

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ı will do differantial expression analysis and some visualization procesess on R program but ı havenot road map for it so ı assumed that ı can do it on my own computers.

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sam files are text files. bgzip it while keeping the originals. MD5sum the bgzip files. Upload both bgzip files and their hashes.

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