Results Gene counts total 0.0 Total annotated reads = 0

[paulineBazelle]

Hello, I'm using TEcount on my data (which has been star mapped with Ensembl GrCH38). For TEcount I use : --TE: GRCh38_Ensembl_rmsk_TE.gtf.ind --GTF: Homo_sapiens.GRCh38.110.gtf

For all my samples I get this result

TE counts total 0.0 Gene counts total 0.0

Total annotated reads = 0 Total non-uniquely mapped reads = 731453 Total unannotated reads = 1001107

Is this normal?

Thank you,

Best, Pauline

[olivertam]

Hi,

Thank you for your interest in the software. This is certainly not a normal output. Might I ask you to provide the BAM headers?

$ samtools view -H [BAM]

Thanks.

[paulineBazelle]

HI,

Yes sure Thank you

[image: image.png]

Best, Pauline

Le mar. 19 déc. 2023 à 09:00, Oliver Tam @.***> a écrit :

Hi,

Thank you for your interest in the software. This is certainly not a normal output. Might I ask you to provide the BAM headers?

$ samtools view -H [BAM]

Thanks.

— Reply to this email directly, view it on GitHub https://github.com/mhammell-laboratory/TEtranscripts/issues/169#issuecomment-1863146396, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD7A54RPL2VET4LPXYG2HG3YKHBZXAVCNFSM6AAAAABA3PZKI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRTGE2DMMZZGY . You are receiving this because you authored the thread.Message ID: @.***>

[olivertam]

Hi,

I'm afraid the image did not come through. Do you mind pasting the output?

Thanks.

[paulineBazelle]

Hi,

@HD     VN:1.6  SO:coordinate
@SQ     SN:ENST00000473358      LN:712
@SQ     SN:ENST00000469289      LN:535
@SQ     SN:ENST00000417324      LN:1187
@SQ     SN:ENST00000461467      LN:590
@SQ     SN:ENST00000641515      LN:2618
@SQ     SN:ENST00000335137      LN:1054
@SQ     SN:ENST00000466430      LN:2748
@SQ     SN:ENST00000495576      LN:1319
@SQ     SN:ENST00000477740      LN:491

Thanks, Pauline

[olivertam]

Hi,

It appears that you have mapped your reads onto the Ensembl transcripts (as shown by the ENST in the name), rather than the GRCh38 genome. Since TEcount uses genomic alignments to annotate against genes & TE, it will not work with this BAM file. You will need to re-align with STAR onto the GRCh38 Ensembl genome in order to use TEcount.

Thanks.

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