Sefi196
commented
1 month ago Hi Domivka,
Glad to hear IsoLamp is of interest to you.
Yes your right, IsoLamp was designed for amplicon data so its functionality is limited when it comes to whole transcritome and single cell data. It is possible to modify the code to perform whole transcriptome analysis but my suggestion would be to just use bambu on its own.
In saying this i have tried taking single-cell long read data and identifying isoforms for genes of interest, (however this needs to be done one gene at a time). This works well for some genes but is often poor for more complex genes especially where the reads are not full length or there is alot of internal priming. Also something to consider is that with single cell long read data the reads need to be demultiplexed and this is something that isolamp cannot do.
Im not sure what your goals are but there are some well established tools for sc LR analsyis such as FLAMES and Isoquant. Perhaps these tools might be more useful?
If you let me know what type of analysis you wish to do perhaps we can add some features to help.
Sefi
Hello!
First of all, thank you for sharing IsoLamp with us.
I see that IsoLamp was created for the targeted sequencing, but I have a small newbie question. I was wondering if it would be possible to apply IsoLamp to the nanopore long-read whole-transcriptome data.
I have data from 17 single-cell samples and would want to try using IsoLamp for this, assuming the parameters file is adjusted with paths to the whole genome reference, etc. The fastq files were previously mapped to the reference genome with minimap2 with -ont flag.
Thanks!