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cancerit / NanoSeq

Analysis software for Nanorate Sequencing (NanoSeq) experiments
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Can efficiency_nanoseq.pl count 'rb' tag correctly? #102

Open monagai opened 1 month ago

monagai commented 1 month ago

Because extract_tags.py sets rb tag not RB, efficiency_nanoseq.pl does not seem to count rb tag correctly. https://github.com/cancerit/NanoSeq/blob/4136d3ca943b96b2cf9013ac14183f098b8234be/perl/efficiency_nanoseq.pl#L149-L154

fa8sanger commented 1 month ago

After running extract_tags.py you need to remap and then run bamaddreadbundles which will add the rb tag correctly

On 7 Aug 2024, at 10:02, Momoko NAGAI @.***> wrote:

Because extract_tags.py sets rb tag not RB, efficiency_nanoseq.pl does not seem to count rb tag correctly. https://github.com/cancerit/NanoSeq/blob/4136d3ca943b96b2cf9013ac14183f098b8234be/perl/efficiency_nanoseq.pl#L149-L154 [github.com]https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cancerit_NanoSeq_blob_4136d3ca943b96b2cf9013ac14183f098b8234be_perl_efficiency-5Fnanoseq.pl-23L149-2DL154&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=F-H_vPRdO8pv0hJFH3n2p5X5CHLXQoKcuKC4fS6RfXyBShTU_PwuLkwV-UiC6EO7&s=Xt7TMLFA7k7a4Fg0X41vA37tUZ_laUnolCVeGCDE2kU&e=

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monagai commented 4 weeks ago

Thank you for your comment.

After running extract_tags.py you need to remap and then run bamaddreadbundles which will add the rb tag correctly

I did so. However, I used NanoSeq 3.5.1. because Nanoseq 3.5.4 sometimes failed for my data. It may be the cause. Thank you.

fa8sanger commented 4 weeks ago

Hi Momoko,

It should have worked. Do you still have the problem?

On 19 Aug 2024, at 03:36, Momoko NAGAI @.***> wrote:

Thank you for your comment.

After running extract_tags.py you need to remap and then run bamaddreadbundles which will add the rb tag correctly

I did so. However, I used NanoSeq 3.5.1. because Nanoseq 3.5.4 sometimes failed for my data. It may be the cause. Thank you.

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cancerit_NanoSeq_issues_102-23issuecomment-2D2295557010&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=DNHk_Pv3LtQkjdhxUAtIozXNDzMbquRN5Sce0ezWN02NshxvUUCOrTmLUUvMICKb&s=eIHOFeX32owz3L2pE_Cp1h_zYUVO5N4kPoh2zyrTXnY&e=, or unsubscribe [github.com]https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADNUT3JAYOE3PNYHCMO4NKTZSFK2XAVCNFSM6AAAAABMD6OVMCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJVGU2TOMBRGA&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=DNHk_Pv3LtQkjdhxUAtIozXNDzMbquRN5Sce0ezWN02NshxvUUCOrTmLUUvMICKb&s=0ICdAR9_M97W9HQHsCOoTdjpv9RA51BJLuRqsy9JzhA&e=. You are receiving this because you commented.Message ID: @.***>

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monagai commented 4 weeks ago

It should have worked. Do you still have the problem?

Thank you for your comment. It may be a problem of our data, not NanoSeq. Sorry, I have not investigated the problem deeply yet.