Hello all, I have downloaded GENCODE and RefSeq transcripts and I want to combine these and filter for redundancy. Please suggest me how to proceed. Thank you
with seqkit:
$ seqkit rmdup -w 0 -s -i test.fa --quiet
output:
>uc001aal.1 CDS=1-916
ATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCAC
>uc001aak.4
CACACAACGGGGTTTCGGGGCTGTGGACCCTGTGCCAGGAAAGGAAGGGCGCAGCTCCTGCAATGCGGAGCAGCCAGGGCAGTGGGCACCAGGCTTTAGCCTCCCTTTCTCACCCTACAGAGGGCAG
>XM_017003010.1 CDS=512-893
AAATATGGGATTCCTGGGTTTAAAAGTATAAAATAAATATGTTTAATTTGTTAACTGATTACTATCAGAATTGTACTGTTCTGTATCCCACCAGCAATGTCTAGGAATGCCTGTTTCTCCACAAAGTGTTT
Input:
$ cat test.fa
>uc001aal.1 CDS=1-916
ATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCAC
>uc001aak.4
CACACAACGGGGTTTCGGGGCTGTGGACCCTGTGCCAGGAAAGGAAGGGCGCAGCTCCTGCAATGCGGAGCAGCCAGGGCAGTGGGCACCAGGCTTTAGCCTCCCTTTCTCACCCTACAGAGGGCAG
>NM_001005484.1 CDS=1-916
ATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCAC
>XM_017003010.1 CDS=512-893
AAATATGGGATTCCTGGGTTTAAAAGTATAAAATAAATATGTTTAATTTGTTAACTGATTACTATCAGAATTGTACTGTTCTGTATCCCACCAGCAATGTCTAGGAATGCCTGTTTCTCCACAAAGTGTTT
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version 2.3.6
Please post example input (one or two eg from gencode and refseq) and expected output.
Cluster the sequences with CD-HIT
The above two sequences are from GENCODE nad the last two sequences are from RefSeq so there are total four sequences, first sequence and third sequence are redundant but they have different id. I want one of these two sequence to be removed while merging.The result should be like this
If it is ok for you to run legacy blast then this link could be of use https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html
see compare two fasta files