list index out of range about syri HOT 8 CLOSED

Hi, thanks for sharing the details. It seems that you are using Python3.7. Can you please try it again with python 3.5? Some libraries have been changed between Python3.5 and 3.7 which sometimes result in unexpected errors. I would guess that using Python3.5 might be able to fix the problem.

from syri.

Hi, thanks for replying. I got the same errors when using Python3.5.

from syri.

Do you think the whole chromosome inversion can make such an issue?

from syri.

Whole chromosome inversions is not a typical use case. So, it is possible that that there is some uncaught exception. From the output files, it indeed seems that for most chromosomes no syntenic region was identified. If this is indeed the problem, then you can easily solve this by reverse-complimenting the chromosomes for which no syntenic regions were found.

If the problem still persists, then it would be great to see the log file as well as a sample bam file (one chromosome) which can be used to reproduce this error.

from syri.

Thanks. It works now after reverse-complementing the chromosomes with whole chromosome inversion.

I am wondering if I need to adjust the start/end for genome B in syri.out?

from syri.

Hi. Good to know that it worked for you.
I would recommend that you reverse complement these "inverted" chromosomes in the fasta file itself. Then, you can do alignment and run SyRI again. This will ensure that the coordinates in syri.out are as per the reverse complemented chromosomes and would reduce chances of errors.

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Thanks.
Yes, I did the same as you recommended.
Because the genomes I used to analyzed have been published, if I reverse complemented the original fasta files, the syri.out just record the coordinates of the reverse complemented chromosomes.

I think if I would like to get the coordinates of the original chromosomes, I should adjust the coordinates. Since I only reverse complemented the genome B, what I need to do is adjust the coordinates of chromosomes in genome B.

In my case, I would only summarize the rearrangements for the reference genome A. It would be OK whatever the coordinates of chromosomes in genome B like.

If people want to draw a local rearrangement between genome A and genomeB, I think they should use the coordinates from the original genome so that they can compare with the previous study. Do you think so?

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It is not possible for me to comment on this.

You are correct in that the coordinates of the genome A would not change, and that you can reverse complement the coordinates from syri.out to get the original fasta file coordinates. However, it is upto you to decide how you want to report and represent this information :)

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