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adnaniazi / tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
https://www.cbu.uib.no/valen/
GNU General Public License v3.0
53 stars 18 forks source link

fast5 format problem #65

Open peipeizhang123 opened 10 months ago

peipeizhang123 commented 10 months ago

my fast5 format dispaly follow when I enter command line h5ls -r FAW63410_pass_08e163a6_709ba1bb_9.fast5,cannot be recognized by tailfindr,How to solve this problem

/                        Group
/read_000aea75-ac28-486f-8248-170a5feb363c Group
/read_000aea75-ac28-486f-8248-170a5feb363c/Raw Group
/read_000aea75-ac28-486f-8248-170a5feb363c/Raw/Signal Dataset {24738/Inf}
/read_000aea75-ac28-486f-8248-170a5feb363c/channel_id Group
/read_000aea75-ac28-486f-8248-170a5feb363c/context_tags Group
/read_000aea75-ac28-486f-8248-170a5feb363c/tracking_id Group
/read_000d8dc8-952f-403a-934a-fecc1587c51d Group
/read_000d8dc8-952f-403a-934a-fecc1587c51d/Raw Group
/read_000d8dc8-952f-403a-934a-fecc1587c51d/Raw/Signal Dataset {53336/Inf}
/read_000d8dc8-952f-403a-934a-fecc1587c51d/channel_id Group
/read_000d8dc8-952f-403a-934a-fecc1587c51d/context_tags Group, same as /read_000aea75-ac28-486f-8248-170a5feb363c/context_tags
/read_000d8dc8-952f-403a-934a-fecc1587c51d/tracking_id Group, same as /read_000aea75-ac28-486f-8248-170a5feb363c/tracking_id
/read_001edc50-4be8-4ed1-8dbc-742ac2883216 Group
/read_001edc50-4be8-4ed1-8dbc-742ac2883216/Raw Group
/read_001edc50-4be8-4ed1-8dbc-742ac2883216/Raw/Signal Dataset {22592/Inf}
/read_001edc50-4be8-4ed1-8dbc-742ac2883216/channel_id Group
/read_001edc50-4be8-4ed1-8dbc-742ac2883216/context_tags Group, same as /read_000aea75-ac28-486f-8248-170a5feb363c/context_tags
/read_001edc50-4be8-4ed1-8dbc-742ac2883216/tracking_id Group, same as /read_000aea75-ac28-486f-8248-170a5feb363c/tracking_id
adnaniazi commented 10 months ago

Hi,

It seems like your Fast5 files are not basecalled. Make sure that you basecall them using --fast_out option in Guppy. This will create a new set of fast5 files with the basecalling information. Use that as input to tailfindr

Alternatively, you can also convert your fast5 files to pod5, basecall pod5 filesusing dorado and doardo can produced polyA estimates for you during basecalling. Please read dorado documentation on how to do it.

On Fri, Jan 19, 2024, 4:07 AM peipeizhang123 @.***> wrote:

Hi，Dear author， I have recall my fast5 data with Guppy v6.2.1. The tool tailfindr can be running normally. But I met another problem, my result csv file is empty,I cannot get Poly length. image.png (view on web) https://github.com/adnaniazi/tailfindr/assets/41148240/01bd53e1-9647-499d-9227-3c8ca08abec0

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