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Bam files generated by TopHat are incompatible with feature counting software such as HTSeq-count. The reason is likely due to the change to samtools. Tophat uses old samtools 0.1.18. Currently I have to convert bam files to sam and then back to bam with samtools 1.6 to make the suitable for HTSeq-count and subsequent differential gene expression analysis.
Example of the error that HTSeq-count gives on bam files from TopHat
Error occured when reading beginning of SAM/BAM file.
'csamtools.AlignedRead' object has no attribute 'reference_start'
[Exception type: AttributeError, raised in _HTSeq.pyx:1357]
The text was updated successfully, but these errors were encountered:
Bam files generated by TopHat are incompatible with feature counting software such as HTSeq-count. The reason is likely due to the change to samtools. Tophat uses old samtools 0.1.18. Currently I have to convert bam files to sam and then back to bam with samtools 1.6 to make the suitable for HTSeq-count and subsequent differential gene expression analysis.
Example of the error that HTSeq-count gives on bam files from TopHat
Error occured when reading beginning of SAM/BAM file.
'csamtools.AlignedRead' object has no attribute 'reference_start'
[Exception type: AttributeError, raised in _HTSeq.pyx:1357]
The text was updated successfully, but these errors were encountered: