Single-end reads for MAJIQ

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Greg Chik

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May 21, 2021, 1:30:20 PMMay 21
to majiq_voila
Hi,

I wanted to ask about whether single end reads are good enough to study alternative splicing using MAJIQ. I have about 15 individuals who I have stem cells and stem cell-derived derivatives, but the data is single-end reads. I heard that this might not be as good as paired-end reads, but I wanted to ask if one can use single-end reads to detect differential splice junction usage. Are there other considerations about library preparation?

Thanks

Matthew Gazzara

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Jun 15, 2021, 11:25:25 AMJun 15
to majiq_voila
Hello and thanks for your interest. Paired-end reads tend to be better just because they generally have more uniquely mapped and splice junction reads (the only ones MAJIQ considers). However, MAJIQ can handle single-end reads just fine as well. 

Other other thing to consider. Sequencing depth is very important where more is better. What sort of depth is your 15 samples? Typically the lower bounds is something like 20M reads. Finally if your library is strand specific (forward or reverse), MAJIQ can account for this as well. This information is given to the MAJIQ Build command through the configuration file. More information on that is in the documentation on the configuration files here: https://biociphers.bitbucket.io/majiq/quick.html#conf_file

Let me know if you have any more questions! 

Best,
Matt
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