Open Xuyuch opened 3 hours ago
Hi Yuchen, Can you show me the first few lines of the index? The format of index looks like this:
>AAACGAAAGAAACGCC
AAACGAAAGAAACGCC
>AAACGAAAGAAAGCAG
AAACGAAAGAAAGCAG
Oh I know the reason now. In my version of index, it looks like this
>barcode_1
ACAGCGGGTGTGTTAC
>barcode_2
ACAGCGGGTTGTTCTT
>barcode_3
ACAGCGGGTAACAGGC
>barcode_4
ACAGCGGGTGCGCGAA
>barcode_5
ACAGCGGGTCCTCCAT
>barcode_6
ACAGCGGGTCATGGTT
I will modified to your version and test it. Thank you! Yuchen
Hi Yang, I was testing the codes and found error when I do convert_hic2. And I do believe the problem comes from this part:
Here, I think the barcode file was changed from txt file to a fa file and use bowtie to index the file. So I tried manually name those barcode as barcode_# and create a 737K-arc-v1.fa (enclosed here737K-arc-v1.fa.txt). However, even though the bowtie gives a good result, the convert_hic2 get a Segmentation fault (core dumped)
Could you please help me solve this issue? Or could you share the 737k-arc -v1 bowtie index you used in your pipeline? Thank you!
Best, Yuchen