Hi,
I have a merged fastq file which contains reads from multiple samples with thermo barcodes. I want to demultiplex this file into corresponding fastq files based on the barcodes. However these barcodes are not exactly coming in the beginning of 5' end of the read. They are coming after some bases in each read as shown below:
ATATTTGTCGCCTTTGGTTAGCAGTTGCGTGTTGCTAAGGTTAAACGTAACTTCATTGTCCCTGAACAGCACCTCCATCTCATCCCTGCGTGTCTCCGACTCAGTTCCGAAGTCACGATGGTGTGTGGAGGATAGAGACTGAAAAAGGAGCTGAAACATACAGGGTATTCATTCTACTTCCACTTCCCCAGTGTGTCAGGGTTAACACTGGATATGCGTACACATGTCCACACATGCAGGCACACGAATACATACATACATACTTCCCATACATATGCACCCACACACCATCACCGACTGCCCATAGAGAGGAAAGCGGAGGCGTAGTGGAGGTGCTGTTCAGGGAACAAACCAAGTTACGTTTAACCTTAGCAATACGTT
GTGTTATGTAACCTTACTTCAACAACTCAGTTTTTACGTATTGCTAAGGTTAAACGTAACTTGGTTTGTTCCTGAACAGCACCTCCATCTCATCCCTGCGTGTCTCCGACTCAGTCAGGCCGAACGATGGTGTGTGGGCAGGGATGCCCCATACAACTTTACTCAGATCTTGGAACTTTAGATGCTGTCCAACTCCCAAAGAAATAACAATTACTCACTGCAGGGGACACCAGAAGGGAGACACTTTTATTATTAGAGGAAATTCCCTGGTGGAAAGAGCAGCTAAGGCCACAACTAAGGAAACTCAACAAACTCAAAGATAAAACCAGTAAGTAATTCAAATGCCCATCAATGATAGACTGGATACAGAAAATGTGGCACATATACACCACGGAATACCATGCAGCCATAAAAAAGGATGAGTTCATGTACTTTGCACGGACATGGATGAAGCTGGAAACCATCATTCTTTGGCAAAACAACACAGGAACAGAAAACCGAACACTGCACGTTCTCATTCATAAATGGGAGTTGAACAATGAGAACACATGGACACAGGGAGGGGCACACCACACACCATCGTCCATTGCAAGCTGAGTGGGAGCACGAGGTGCTGTTCAGGGAACAAACCAAGTTACGTTTAACCTTAGCAATACGTGG
The above is just an example.
I want to know if there are any specific tools for this purpose. I have tried Flexbar, however the results were not satisfactory. Moreover, there are high chances of errors in the barcodes of the reads. So I have to deal with that as well. These are single ended reads and not paired.
Please suggest any good tool or a solution.
Thanks
Do you need to keep the sequece before the barcode (they look like adaptor sequences to me).
If not, then use a tool like cutadapt to trim off the 5' adaptor sequences and then a standard demultiplexing tool (such as fastx) to demultiplex them.
cutadapt can demultiplex during the trim as well. It seems to work well for this case.
Would these be 3' adapters?