Can't find transcript ids from fasta in bed

[XMTian]

Hi,

I tried to use how_are_we_stranded_here to figure out the strands of my RNA-seq data.

Here are my commands:

check_strandedness --gtf Midas.annotation.v2.6.gtf -r1 Aast_14_trimmed_R1.fq.gz -r2 Aast_14_trimmed_R2.fq.gz -fa Midas.2.6.transcripts.fa

Here is how the gtf file looks like.

head Midas.annotation.v2.6.gtf

1 funannotate transcript 6208 30525 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 6208 6471 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 7462 7555 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 16749 16855 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 17474 17511 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 17707 17785 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 17863 17957 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 18669 18714 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 18793 18939 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";
1 funannotate exon 19209 19291 . + . transcript_id "Midas_000001-T2"; gene_id "Midas_000001";

How Midas.2.6.transcripts.fa looks like.

>Midas_000001-T1
AAAAAAAAAAAAAAAAAAAAAAATTCGGCTTATACTGCAGCTTAGAAGTCGTGCTCAGAGGAACGAGCTTTATCCCACTGCATTTCGGGCAGGTTAGAAGTCGTGCCGAGTAACGAAAAAAAAGAGGGAATTCGTGTTCATGAGCACGAATCAATAGATTAAATTTCGTT
>Midas_000001-T2
CTGACGAAGTGTCCTGATGCGATCCACGTCCCATTTTTACGACGGAGACCGCTTGCTGACGGCAGCCGGTTGCCATAACGTCCCTCCAGCAACATGTCCTCGTCGGGGGCGCAGCGTGTCGGTCCCGCGGCGGCTTTCCCAGAGAACCAGGGCGGTGCGGCGGCGGCAGG
>Midas_000002-T1
CATAACTCAAAAAACCATCAGTGAAGTCACAGCTGCTAGTCTTTGGAGCAGATCTCAATAAAAACCACAGCTTGTCCTCATCTCATGGCCTCATCCTCTCTCTGCAGCTGCAGGCGTGGTGGACTTGAACCTGTGCAACATCCGGGACATGGAGGTCATCGAGCTGAGCA
>Midas_000003-T1
GTGTCATTCACAATAAAAATCAGAGCAGCTTGGACTTGCATCCAAACAGAACACCATCAAAGTAGAAGAAGCACCAGATGACGACCTGTAGCTTTTCAAACACCTGAAGTTCAGCTTTCTGACAGGAGCCATCAGGCCTGAACCTCCAGCACTGCCTAAGGAGCCTTCAA
>Midas_000004-T1
ATGACAGAGAGAGATAGACTAGAGCTGAGGAGACCGCCATGGAGAGAGAGAGGACAGAGAAGAGCGAGACAGAGAGCGATACATACAGAGAGAGAGACCGCCAGAGAGAGAGACCCCGACCGAGAGAGCGGCGACGACCGAGAGGCGCGCACAACAGCACATAGAGAGAG
>Midas_000005-T1
CTGGACTGGACCAGAGCGACATCATGAAGCTGCTGAGACACGGCATCTACACTCTGCTGGTAATTTGCAGTGTATTGTGGGCTTCTTGCTCCAAGGTTAAAGCTGAATCATCTCCTGGATGTGACACCACCTTGACGTTCTCCTCAGAATTGAGCACCTTGACTGAAGGA
>Midas_000006-T1
GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGCGAGCGAGCGAGCGAGCACGCGCACGCAGCAGGTCAAACTCGCTGACAACAGGTCCAAAGACCCGGACAGAAAAACAATAGAAGAGAGTAGAAAATGAGTGGTGCAG
>Midas_000007-T1
GTAAGCCAGCAGTCTGAGAGTGAAGTGCTCTGTTGGGGTGATACAGTACTATGAGGTCTTTGAAATAAGATGGGGCCTGATTATTCAAGACCTTTTTGCATTTGTTCTGGGACCCCTGTGTCCTCATGCATGGAAATACAGAGGCGAGGGGAGAAGCAGCACCACCACCT

But I got this error, I checked the transcript ids, there are all in the fasta file.

Results stored in: stranded_test_Aast_14_trimmed_R1_2
converting gtf to bed
Checking if fasta headers and bed file transcript_ids match...
Can't find transcript ids from Midas.2.6.transcripts.fa in stranded_test_Aast_14_trimmed_R1_2/Midas.annotation.v2.6.bed
Trying to converting fasta header format to match transcript ids to the BED file...
Can't find any of the first 10 BED transcript_ids in fasta file... Check that these match

Could you help me to figure it out?

Best,
Xiaomeng

[LauraPugh]

Hi,

I get the same error. Did you find a solution?

[OlivierBakker]

Hi,

Just bumping this as I am also running into the same issue and there doesn't seem to be a solution. I re-generated the cdna fasta based on the Ensembl 99 gtf file. I also manually checked the first 10 records, and they are definitely in there. Would love an update on this.

[signalbash]

I think this was an issue with formatting. I've edited the code to strip whitespace and it tentatively works locally on the Midas transcriptome/gtf examples you gave.
0fedf92

[KristinaGagalova]

Hi,
I am using the pip version of the tool and I am having the same issue. Would be possible to update this bug fix in all versions? The commit that you are pointing to works well