Closed dfajar2 closed 5 years ago
Right, this is a common problem associated with the needle alignment program we have used in CRISPResso. We have a new version of CRISPResso2 with our custom alignment to test here: crispresso2.pinellolab.org Could you please let us know if you also observe the same problem with this new version?
Will do and thanks again
Just to let you know that I just tested CRISPResso2 and it fixes this alignment problem. Is the code publicly available yet?
Great, not yet we are finalizing it before publication, for now, please use the website and please let us know if you encounter any problems.
On Wed, Aug 29, 2018 at 12:49 PM dfajar2 notifications@github.com wrote:
Just to let you know that I just tested CRISPResso2 and it fixes this alignment problem. Is the code publicly available yet?
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Perfect. Thanks!
Great! Really looking forward to release of v2!!
Now it is available https://github.com/pinellolab/crispresso2
Hi Luca,
First of all thanks for developing this pipeline.
I have a question for you. I'm pasting below two of the alleles from the "Alleles_frequency_table_around_cut_site" file.
Aligned_Sequence Reference_Sequence Unedited %Reads #Reads GACTGTAAGTGAATTACTTTTTTTGTCAATCA----ACCATCTTTAACCTAAAAGAGTTT GACTGTAAGTGAATTACTTTTTTTGTCAATCATTTAACCATCTTTAACCTAAAAGAGTTT True 0.24111800019683108 49 GACTGTAAGTGAATTACTTTTTTTGTCAATC----AACCATCTTTAACCTAAAAGAGTTT GACTGTAAGTGAATTACTTTTTTTGTCAATCATTTAACCATCTTTAACCTAAAAGAGTTT True 0.16730636748351543 34
As you can see, they are exactly the same except for the A which can align to either side. This reminds me to the LeftAlignAndTrimVariants module from GATK which in cases like this, simplifies the output by aligning those bases always to the left. Is it possible to improve the alignment in CRISPResso, so they are grouped as the same event?
Thanks