[~warn] Warning, zero reads pseudoaligned check your input files and index,

[creat-star-stu]

Here is the English translation of the provided text:

Excuse me, for a single gene with three transcripts (including one mRNA sequences on NCBI whose names start with LOC), after establishing the index with kallisto: kallisto inspect PCindex.idx

[index] k-mer length: 31
[index] number of targets: 1
[index] number of k-mers: 660
[index] number of equivalence classes: 1
#[inspect] Index version number = 10
#[inspect] k = 31
#[inspect] number of targets = 1
#[inspect] number of equivalence classes = 1
#[inspect] number of contigs = 1
#[inspect] Number of k-mers in index = 660
#EC.size        Num.targets
1       1

#EC.size        Num.kmers
1       660

Then, using quant: kallisto quant -i ./PCindex.idx -o ./3kallisto/paired_out1 --bias -t 8 ./SRR70XX_forward_paired_R1.fq.gz ./SRR70XX_forward_paired_R2.fq.gz

The results show: [quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 1
[index] number of k-mers: 660
[index] number of equivalence classes: 1
[quant] running in paired-end mode
[quant] will process pair 1: ./SRR70xxx_forward_paired_R1.fq.gz
./SRR70xxx_forward_paired_R2.fq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] learning parameters for sequence specific bias
[quant] processed 22,172,671 reads, 0 reads pseudoaligned
[~warn] no reads pseudoaligned.
[quant] estimated average fragment length: 0
[em] quantifying the abundances ... done
[em] the Expectation-Maximization algorithm ran for 52 rounds
[~warn] Warning, zero reads pseudoaligned check your input files and index

I have checked all the previous steps and they are fine, but I still get an error for this gene. What should I do?

[Yenaled]

There is nothing wrong. Your sequencing data simply does not have that gene in it.

[creat-star-stu]

Thank you very much for answering my questions. Thank you again ---- Replied Message ---- FromDelaney ***@***.***>Date12/22/2024 ***@***.***>***@***.***>, ***@***.***>SubjectRe: [pachterlab/kallisto] [~warn] Warning, zero reads pseudoaligned check your input files and index, (Issue #473) There is nothing wrong. Your sequencing data simply does not have that gene in it. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>