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gaoyubang / nanom6A

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emp #14

Open yuxinPenny opened 2 years ago

yuxinPenny commented 2 years ago

Dear author, I have completed nanom6A running and got the results. However, in the ratio.tsv file, the gene name and chrom number is missing and in the genome_abundance.bed, the gene name is NA as well. Does the reference transcriptome matters? I used the human transcripts reference downloaded from Gencode. If no gene name can be matched, does adding a -b parameter helps?

PS. command: cd /home/yuxin/2021Fall/hm_tmp/HMEC_WT/guppy/workspace find /home/yuxin/2021Fall/hm_tmp/HMEC_WT/guppy/workspace -name "*.fast5" > /home/yuxin/2021Fall/hm_tmp/HMEC_WT/nanom6A_result/fast5_file.txt

python3 /home/yuxin/nanom6A_2021_3_18/extract_raw_and_feature_fast.py --cpu=5 --fl=/home/yuxin/2021Fall/hm_tmp/HMEC_WT/nanom6A_result/fast5_file.txt -o /home/yuxin/2021Fall/hm_tmp/HMEC_WT/nanom6A_result --clip=10

python3 /home/yuxin/nanom6A_2021_3_18/predict_sites.py \ -i /home/yuxin/2021Fall/hm_tmp/HMEC_WT/nanom6A_result \ -o /home/yuxin/2021Fall/hm_tmp/HMEC_WT/nanom6A_result/result \ -g /home/yuxin/2021Fall/hm_tmp/HomoSapiens/hg38.fa \ -r /home/yuxin/2021Fall/hm_tmp/HomoSapiens/gencode.v29.transcripts_simplified.fa \ --model /home/yuxin/nanom6A_2021_3_18/bin/model

head of transcriptome reference:

ENST00000456328.2 GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTC TCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGA TGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTG CAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGG GCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCAT AGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAACCTAGGCCAG TGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACG ACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGCAGGGCCATCA GGCACCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTG

gaoyubang commented 2 years ago

Can you post your extract.reference.isoform.bed12 and extract.reference.bed12 file?

yuxinPenny commented 2 years ago

I don't have this two file, actually.

yuxinPenny commented 2 years ago

I got an empty extract.bed6.gene file and several normal extract.xxx file.

gaoyubang commented 2 years ago

Please add -b parameter

gaoyubang commented 2 years ago

We update the nanom6A version, the newest version is nanom6A_2021_10_22.tar.gz.

yuxinPenny commented 2 years ago

Where can I download the -b gene information files?

gaoyubang commented 2 years ago

You can make it by yourself. The format is:

GeneID isoformID1 isoformID2

AT1G51370 AT1G51370.2 AT1G51370.1 AT1G51370.3 AT1G50920 AT1G50920.1