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STAR Alignment Trouble

Hello,

I'm trying to run a STAR alignment on some RNA-Seq reads but my sam output file is much smaller than expected to the point where I believe it didn't work correctly. I'm not sure what I'm doing wrong.

This is the command I used

STAR --runThreadN 4 --genomeDir /Path/To/Index --readFilesCommand gunzip -c /Path/to/Reads/File

Please let me know if there is any other information I can provide. Any help would be appreciated, Thank you in advance!

star alignment rna-seq
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updated by Sergey Naumenko Sergey Naumenko • written by atcggcta • atcggcta

Hi,

can you try this instead:

STAR --runThreadN 4 --genomeDir /Path/To/Index --readFilesCommand gunzip -c --readFilesIn /Path/to/Reads/File

I had a similar problem like yours where I forgot to place the "readFilesIn" parameter.

• 0 views • link
written by gasta88 • gasta88

Thank you, that was the issue!

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written by atcggcta • atcggcta

1 answer

Hi!

It is hard to guess. Maybe you are mapping to the wrong reference, or you sample is contaminated? Do you see any error messages from STAR? What is your mapping statistics?

Maybe try to add --outReadsUnmapped Fastx to see how big are unmapped files?

Other parameters you might find useful: rnaseq.star.sh

Sergey

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written by Sergey Naumenko Sergey Naumenko

Hello Sergey,

Thank you for the response

I will try your suggestions. I did get two messages but I didn't know what they meant (I totally forgot to mention that)

They were

"gzip: Read1.gz: No such file or directory"

and

"gzip: Read2.gz: No such file or directory"

• 0 views • link
written by atcggcta • atcggcta

It looks like it can't find your input files. Check the path - it is case sensitive.

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written by Sergey Naumenko Sergey Naumenko

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