counting the unmapped reads
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9.2 years ago
zizigolu ★ 4.3k

Hi all,

I have a sam file, my supervisor asked me to count the number of unmapped reads, which command I should use?

samtools view -c -F 4 [file.sam] says that input is probably truncated

RNA-Seq • 5.4k views
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Your file is corrupt, my friend. As mentioned above, the command is fine.

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Are you Iranian, Amir?

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15 months ago

Hi all,

I have a sam file, my supervisor asked me to count the number of unmapped reads, which command I should use?

samtools view -c -F 4 [file.sam] says that input is probably truncated

The command above would give you the number of mapped reads . if you want to get unmapped reads you should use "-f" not "-F"

samtools view -c -f 4 [file.sam]
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9.2 years ago

Your command is fine, the file isn't. Ask your supervisor to double check that the file isn't corrupt.

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Devon,

He's just waiting for the result I can't report any error.

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The file is corrupt, you can't give him a reliable result.

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ok thank you

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If you've downloaded the file from somewhere you can try downloading again.

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