How To Determine If Library Is Strand-Specific
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8.5 years ago
predeus ★ 1.6k

Hello all,

this might be a very basic question but I gave it some thought and don't see a satisfactory answer.

Let's say I have a FASTQ file from a sequencing experiment. How can one quickly determine if the given library is strand-specific?

On a related note, how important is it for the alignment (either Tophat or Bowtie) to specify if the library is strand-specific, for both single-end and paired-end reads?

Thank you in advance.

sequencing strand paired-end • 6.3k views
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8.5 years ago
JC 12k

The best way is to keep record of the sample preparation. But if you only have the Fastq file(s), you can map a few randomly selected reads (sometimes I run test with 1 million reads) and you must see a bias in the orientation, many of your reads will be f-f or r-r with the expected gene.

Using strand-specific information in mapping improves the resolution of multimapped reads and antisense overlapped genes.

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After mapping some reads you could also use infer_experiment from the rseqc package. It will give you fractions how many reads map on the same strand as in a supplied annotation.

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Same answer as JC, written specifically for Tophat http://tophat.cbcb.umd.edu/faq.html#library_type

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Thank you everybody! This is very helpful.

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Similar question: Do I understand correctly that counting number of reads with flags 67 and 83 should give me strong bias over one or another when using strand-specific paired-end data?

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