seqkit amplicon only keeps one amplicon  #191

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1. shenwei356 commented on Feb 23, 2021

   

   shenwei356

   on Feb 23, 2021

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   Right, PCR could produce all combinations of the forward and backward primers. We should output them too.
2. shenwei356

   added

   enhancement

   on Feb 23, 2021
3. mlosilla commented on Feb 23, 2021

   

   mlosilla

   on Feb 23, 2021

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   yeah exactly.

   In my case, the positions in the bed file would be enough. I would choose the amplicon I want and use the positions as trimming points for my fastq reads--but the sequences of the PCR products may be useful for other users.

   Thank you for considering it!
4. shenwei356 commented on Mar 1, 2021

   

   shenwei356

   on Mar 1, 2021

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   In my case, the positions in the bed file would be enough.

   Oh, you can use seqkit loate first, which outputs BED format.
5. zjhzxjm commented on Nov 3, 2022

   

   zjhzxjm

   on Nov 3, 2022

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   期待这个功能早日上线
6. magbio commented on Apr 3, 2024

   

   magbio

   on Apr 3, 2024

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   Hi, I have the same issue here. Outputting the largest amplicon only was misleading in my case, as I was looking for an amplicon within repititive RNA genes of an eukaryotic genome. Instead of predicting a correct PCR amplicon of size around 400bp, seqkit amplicon produced an amplicon of ~50 Kb which does not make any sense in my case.

   As a solution, I see that outputting all valid amplicons is the best option, or you may add an option expected_amplicon_size to give this length a priority or to make an upper limit for the amplicon prediction.

   Here is a toy example

   echo -ne ">seq\nAGTACCTTGGTAGGAGTTTCCTGCTAATGATAAGAATGATATTGGACTAAGTAATGTTGCAAATATAGAAACTGAT\n" | seqkit amplicon -F GGTAGG -R ATCAG
   

   echo  "AGTACCTTGGTAGGAGTTTCCTGCTAATGATAAGAATGATATTGGACTAAGTAATGTTGCAAATATAGAAACTGAT" > seq 
   echo -ne ">seq\n" > multi_seq.fa 
   for seq in {1..10}; do cat seq >> multi_seq.fa; done 
   cat multi_seq.fa | seqkit amplicon -F GGTAGG -R ATCAG | seqkit stats 
   

   • just seen that others have raised the same issue as well seqkit amplicon function #384