Open Bianzh1024 opened 8 months ago
I download the transcriptome fasta from uscs, https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/mrna.fa.gz . when I used kallisto index to bulid the index for kallisto, that had two warning:
[build] loading fasta file mrna.fa.gz [build] k-mer length: 31 [build] warning: clipped off poly-A tail (longer than 10) from 32479 target sequences [build] warning: replaced 196300 non-ACGUT characters in the input sequence with pseudorandom nucleotides [build] counting k-mers ... done. [build] building target de Bruijn graph ... done [build] creating equivalence classes ... done [build] target de Bruijn graph has 3001158 contigs and contains 263628489 k-mers
And it succeed. Why it showed the clipped and non-ACGUT ? The index is right? I hope you can give me some advice. Thanks！ @pmelsted
Yes it’s fine
Yenaled
commented
8 months ago Yenaled
commented
8 months ago
I download the transcriptome fasta from uscs, https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/mrna.fa.gz . when I used kallisto index to bulid the index for kallisto, that had two warning:
[build] loading fasta file mrna.fa.gz [build] k-mer length: 31 [build] warning: clipped off poly-A tail (longer than 10) from 32479 target sequences [build] warning: replaced 196300 non-ACGUT characters in the input sequence with pseudorandom nucleotides [build] counting k-mers ... done. [build] building target de Bruijn graph ... done [build] creating equivalence classes ... done [build] target de Bruijn graph has 3001158 contigs and contains 263628489 k-mers
And it succeed. Why it showed the clipped and non-ACGUT ? The index is right?
I hope you can give me some advice. Thanks！ @pmelsted