Confusion about the C3POa_preprocessing.py and C3POa_postprocessing.py results ?

[wlhCNU]

Hello,
I have two questions to ask you :

1. C3POa_preprocessing.py analysis will produce two types of results: R2C2_raw_reads.fastq and No_splint_reads.fastq. Were the No_splint_reads.fastq could aligned to the appropriate genomes directly ? Does the No_splint_reads.fastq have incomplete sequence of splint fasta or cDNA adapter sequences ?

2. C3POa_postprocessing.py analysis will produce one result file: R2C2_full_length_consensus_reads_R2.fasta. Was the meaning of the last numbers of reads name(as shown in the sequence below:377)? the true length of below sequence is subtracted by 377, and the final result is 80. How should we understand the number 80 ?

82d4e633-f330-464b-8c04-bcc093f37174_15.52_2488_2_735_377
GGCGACCAATGAGATCTTACACCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTGAATTTGGTGGGAGCTTTGCTGAACTCCTCTACAGGTTCCGATTGTCTGAAGATGCCCGTCCGGGCTTTGCTAAGACTGGCTCCTGTGCTGCTTGGGAACCCACAGCCGATGGTCATGTGACCACCTCTGCCGAGGGAAACCCACCCTAGAAATGACTGCGGCACAGAACCCTGATGGCAGCAAAGTGAAGGCAGCATTTCTGTTTTGTAACCAATGGAACTCAGTTGCATACGCCTCACTGTGCTTAAAATTCATGTTGAAAATAAGACAGATAACGCTGGTGTTGTCCACGTGTCATATGATGTATAAAACATCAGTTAAAACTCACATTTTGTAACAAAGATTTTGTTTGTTTTCAAAAAAAAAAAAAAAAACATTTGCGTTGATACCACTGCTTAAAG

[rvolden]

1. The No_splint_reads.fastq is just a collection of reads that BLAT couldn't find a splint sequence in. It should theoretically have both splint and smartseq adapters in it, but it could just be that there were too many errors for it to be found by BLAT.

2. The last number in the name after postprocessing should be the length of the sequence after trimming the adapters. We leave the adapters in the final product because if we put UMIs in, we can use them to demux our reads. 80 is just the total length of the 3' and 5' adapters.

[wlhCNU]

Hi,
When I get the postprocessing sequences,what I need to de next is to remove the 3' and 5' adapeters and the ployA tail. Do you have a good implementation or software to do this ? Thanks.

[rvolden]

I've pushed a change that allows for trimming of adapters in postprocessing