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--single-overhang option #230
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Without a reproducible example I'm not sure I understand what is your issue but if I do my guess is as follows: You have a fragment length distribution that make it (numerically) impossible to ever see the 3' end of a transcript with a read coming from the 5' of any fragment:
Also, |
Thank you for the reply and apologize for the lack of clarity. Here is of an example Transcript:
In this example, we have a 75bp Transcript and a 75bp Read. As you can see the Read should align with the reference as it is the same sequence. However when running Kallisto quant, with no --single-overhang the read does not pseudoalign. Interestingly if you add the --single-overhang option there is pseudoalignment. This can occur with any bp length for a reference gene. In the case of a Transcript that is 1500bp, if there is a 75bp read that starts at position 1425 and ends at position 1500, pseudoalignment will not occur unless the --single-overhang option is used. I have read both the paper and the manual. I couldn't find any reason as to why Kallisto is unable to align reads that are positioned at the end of a Transcript. Thank you for your help. |
Hello,
When trying to align reads to to the end of a gene, kallisto is unable to pseudoalign this read. However when using the --single-overhang option, pseudoalignment occurs.
My question is why is it that kallisto cannot pseudoalign sequences that are from the end of a gene and how does the --single-overhang option work?
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