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lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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Left-aligning option #48

Closed dfajar2 closed 5 years ago

dfajar2 commented 5 years ago

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

lucapinello commented 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?

dfajar2 commented 5 years ago

Will do and thanks again

dfajar2 commented 5 years ago

Just to let you know that I just tested CRISPResso2 and it fixes this alignment problem. Is the code publicly available yet?

lucapinello commented 5 years ago

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?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lucapinello/CRISPResso/issues/48#issuecomment-417023943, or mute the thread https://github.com/notifications/unsubscribe-auth/ABB_6nSD0PxUF2VJtVhkYTdzfVsHpeGzks5uVsYLgaJpZM4WPwOZ .

dfajar2 commented 5 years ago

Perfect. Thanks!

cdustinr commented 5 years ago

Great! Really looking forward to release of v2!!

lucapinello commented 5 years ago

Now it is available https://github.com/pinellolab/crispresso2