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Source of soft clipped reads from target sequencing

Below is the alignment of my paired-end reads from targeted sequencing. There are many soft clipped reads as shown from the highlighted region. What do they mean and what are the potential source of these clipped bases? (Reads have been removed for adapter using fastp software). Thanks

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clip reads soft
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written by yliueagle yliueagle

Soft-clipping of sequencing reads allows the masking of portions of the reads that do not align to the genome from end to end

What is difference between soft-clipped and hard-clipped in SAM specification?

Here is a nice post regarding the effect of soft cliping: https://sequencing.qcfail.com/articles/soft-clipping-of-reads-may-add-potentially-unwanted-alignments-to-repetitive-regions/

And here in depth explanation: https://davetang.org/wiki/tiki-index.php?page=SAM

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written by Medhat Medhat

1 answer

you're likely looking at an homozygous deletion; The soft clipped part of the reads would be the sequence in 5' , on the other side of the deletion.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for clarifying and it makes sense. Below I have another locus seems cannot be explained as deletion, as there are many different 'breakpoints'. Do you have an advice? (These are targeted seq reads from tumor sample)

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written by yliueagle yliueagle

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