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ouyang-lab / KARR-seq

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Pairs files #1

Open lcscs12345 opened 7 months ago

lcscs12345 commented 7 months ago

Hi Anthony,

Congratulations on publishing KARR-seq in Nature Biotechnology. I find the new technique facinating and would like to learn more about it.

This is not an issue but a naive question as I am completely new to the Pairs file format. I downloaded this file and found that there are many minus to minus pairs as well as other combinations. As the refseq NM/NR are used for chr1 and chr2 columns, how should I interpret the pairs other than plus to plus?

$ zcat GSM5064755_G1_kethoxal-HepG2_M13_R01.dedup.pairs.gz | cut -f6- | sort | uniq -c

10696136 -      -
 25557 -       +
 56688 +       -
721473 +       +

Thank you! Chun Shen

anton386 commented 7 months ago

Hi Chun Shen,

Thanks for posing the question -- it can be be confusing since the context is not apparent. The method for constructing our cDNA libraries SMARTer Stranded Total RNA-Seq Kit v2–Pico Input Mammalian produces a reverse stranded library, i.e. Read 1 will show up as a negative strand when mapped to the RefSeq transcripts. If you would like to be conservative in your analysis, you can use the negative to negative pairs.

-Anthony