issue with cluster_report

Hi,

I am trying to detect the isoforms as well as the tissue-specific isoforms . We have 4 tissues, each 2 smrt cell sequenced. So 8 files. I have the hq isoseq sequences and the corresponding cluster_report.csv file for each of them (unfortunately at the beginning, we have not run the processing after merging the same tissues, but before). Now when I wanted to run collapse_isoforms_by_sam.py, I merged the 2 samples from the same tissue. 1st, I got the error for duplicate ID since some of the ids were common between the tissue1-file1.fq and tissue1-file2.fq.

Question1: any suggestion for overcoming this issue in a more appropriate way then what I did bellow?

I merged the file1 and file2 of the same tissue, and renamed the fastq headers using

>transcript/AutoIncrementID <rest of the header>

everything went well and I got the collapsed isoforms etc…

Then I wanted to take the next steps for counting and filtering for the degraded 5’ etc., but it asked for the cluster_report.csv which I have for each sample tissue. Now that I have changed the ids, they do not match. So what is the best way to overcome this issue before I go ahead and run the whole processing from the beginning for FLNC and nfl generation etc.

Question2: What is the best way to detect tissue-specific isoforms with such data? Any suggestion?

Thanks for any suggestion,

[Magdoll]

Hi Hamed,

Sorry I did not receive it. Please send it to [e-mail] or give me an email so I can request file upload.

–Liz

[bostanict]

Done, hope this time it went ok and delivered. Please let me know

On Thu, Aug 8, 2019 at 12:21 PM Hamed Bostan [e-mail] wrote:

Hi Liz,

My email is [e-mail]

Cheers, Hamed

On Thu, Aug 8, 2019 at 12:20 PM Elizabeth Tseng [e-mail] wrote:

I did not receive them. Please give me your email to request file upload. -Liz

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Magdoll/cDNA_Cupcake/issues/84?email_source=notifications&email_token=AEOXGSRRCO6QDDU4PIEAUPTQDRBVBA5CNFSM4IETGIM2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34EXJQ#issuecomment-519588774, or mute the thread https://github.com/notifications/unsubscribe-auth/AEOXGSR2LMFB4JTC7YECA53QDRBVBANCNFSM4IETGIMQ .

– Hamed Bostan, PhD Computational Biology and Bioinformatics

– Hamed Bostan, PhD Computational Biology and Bioinformatics