Can I use a CDS file to build kallisto transcriptome index?

Question

[pavelasquezv]

Hi all,

I read in another post that the cDNA file is more recommended than the CDS file as an input file to build a kallisto transcriptome index here. However, I can not find the cDNA file to use as input to build kallisto transcriptome index in the NCBI here:

I would like to perform a gene correlation analysis using TPM. Thus, of these options I thought to use the GCF_002156985.1_Harm_1.0_cds_from_genomic.fna file.

Please let me know what you think about it, or if you recommend another input file.

Many thanks

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GCF_002156985.1_Harm_1.0_assembly_structure/           2019-12-10 17:48    -   
Gnomon_models/                                         2019-12-10 17:48    -   
GCF_002156985.1_Harm_1.0_assembly_report.txt           2019-12-10 17:48   92K  
GCF_002156985.1_Harm_1.0_assembly_stats.txt            2021-12-12 13:56  7.2K  
GCF_002156985.1_Harm_1.0_cds_from_genomic.fna.gz       2019-12-10 17:48  9.0M  
GCF_002156985.1_Harm_1.0_feature_count.txt.gz          2019-12-10 17:48  360   
GCF_002156985.1_Harm_1.0_feature_table.txt.gz          2019-12-10 17:48  1.3M  
GCF_002156985.1_Harm_1.0_genomic.fna.gz                2019-12-10 17:48   95M  
GCF_002156985.1_Harm_1.0_genomic.gbff.gz               2019-12-10 17:48  134M  
GCF_002156985.1_Harm_1.0_genomic.gff.gz                2019-12-10 17:48  5.3M  
GCF_002156985.1_Harm_1.0_genomic.gtf.gz                2019-12-10 17:48  5.0M  
GCF_002156985.1_Harm_1.0_genomic_gaps.txt.gz           2019-12-10 17:48  248K  
GCF_002156985.1_Harm_1.0_protein.faa.gz                2019-12-10 17:48  4.9M  
GCF_002156985.1_Harm_1.0_protein.gpff.gz               2019-12-10 17:48   11M  
GCF_002156985.1_Harm_1.0_pseudo_without_product.fna.gz 2019-12-10 17:48   50K  
GCF_002156985.1_Harm_1.0_rm.out.gz                     2019-12-10 17:48  3.1M  
GCF_002156985.1_Harm_1.0_rm.run                        2019-12-10 17:48  910   
GCF_002156985.1_Harm_1.0_rna.fna.gz                    2019-12-10 17:48   12M  
GCF_002156985.1_Harm_1.0_rna.gbff.gz                   2019-12-10 17:48   32M  
GCF_002156985.1_Harm_1.0_rna_from_genomic.fna.gz       2019-12-10 17:48   13M  
GCF_002156985.1_Harm_1.0_translated_cds.faa.gz         2019-12-10 17:48  6.1M  
Helicoverpa_armigera_AR100_annotation_report.xml       2019-12-10 17:48   68K  
README.txt                                             2020-01-27 16:55   11K  
README_Helicoverpa_armigera_annotation_release_100     2019-12-10 17:48  727   
annotation_hashes.txt                                  2019-12-10 17:48  410   
assembly_status.txt                                    2022-07-20 00:16   14   
md5checksums.txt                                       2022-07-15 22:41  2.7K