How to trim sequence with trimmomatic according to fstqc report
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6 weeks ago
Elizaveta • 0

After fstqc analyses of paired reads, I have 2 reports. Can you explain, please, how to trim them using trimmomatic. I don’t understand what values ​​to specify in CROP, HEADCROP and othersforward reverse

trimmomatic • 305 views
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Can you tell us what kind of samples are these? This does not seem to be normal genomic sequencing. RNAseq with polyA capture perhaps? A simply CROP etc may not be needed/appropriate in this case.

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You mean this?enter image description hereenter image description here

It`s from ENA: SAMN12570783

I guess, I have to find another sample for my training project

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That appears to be from a spatial transcriptomics project. Is that what you intended to use? This would not be appropriate for a good project for someone starting to learn NGS data analysis.

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I think it is not. I found another sample and it seems good for project. enter image description here

I guess HEADCROP should be 13. But I`m not sure about CROP value. Can you help, please. Thanks for your answer

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This is a classic RNAseq sample. This does not need to be HEADCROP'ed but you could, if you simply want to learn how to do it.

See this blog post for more on why the pattern looks like that.

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