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t2t RNAseq alignment with STAR

Hi all,

I'm trying to implement t2t assembly for RNAseq alignment with STAR (using updated t2t gtf). First basic run with default STAR settings yielded poor result for t2t - all metrics are lower compared to hg38. Is this because i need to customize STAR parameters to work with t2t? Does anyone have experience doing the same? Curious what your results were.

Thank you!

star script:

#!/bin/bash

...

STAR --runMode alignReads \
     --genomeDir ./star_index_hg38/star_index/ \
     --readFilesIn ${R1} ${R2} \
     --readFilesCommand zcat \
     --outSAMtype BAM Unsorted \
 --runThreadN 8 \
     --outFileNamePrefix STAR.HC2_HH23.hg38_multiMap/${SAMPLE}/

hg38 vs t2t STAR metrics

chm13 t2t rnaseq
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updated by GenoMax GenoMax • written by eva_u • eva_u

Since one one has commented on this so far I will say that in general T2T genome is going to be of better quality/more complete. Not many use it as default for analysis so you can't go wrong using either. Your plots show the differences to be within a few percentage points of each other, so the differences are not large.

Intuitively it does not seem logical that you would need to use different parameters for a better quality genome. Since your data appears to be RNAseq the regions with genes are likely very similar in both assemblies.

• 0 views • link
written by GenoMax GenoMax

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