比如缺少gene,甚至 mRNA feature都没有。 # stringtie --merge -G F:\RNA-seq\algnment\sme.gff3 -o merged.stringtie.gtf WT.cd1_1.fq_clean.fq.pos.sorted.assembly.gtf WT.cd2_1.fq_clean.fq.pos.sorted.assembly.gtf WT.unc1_1.fq_clean.fq.pos.sorted.assembly.gtf WT.unc2_1.fq_clean.fq....
复制 # stringtie --merge -G F:\RNA-seq\algnment\sme.gff3 -o merged.stringtie.gtf WT.cd1_1.fq_clean.fq.pos.sorted.assembly.gtf WT.cd2_1.fq_clean.fq.pos.sorted.assembly.gtf WT.unc1_1.fq_clean.fq.pos.sorted.assembly.gtf WT.unc2_1.fq_clean.fq.pos.sorted.assembly.gtf # StringTie...
比如缺少 gene,甚至 mRNA feature都没有。 #stringtie--merge-GF:\RNA-seq\algnment\sme.gff3-omerged.stringtie.gtfWT.cd1_1.fq_clean.fq.pos.sorted.assembly.gtfWT.cd2_1.fq_clean.fq.pos.sorted.assembly.gtfWT.unc1_1.fq_clean.fq.pos.sorted.assembly.gtfWT.unc2_1.fq_clean.fq.pos.sorted.ass...
经过这一步的运行,可以得到hq_isoforms.fasta.no5merge.collapsed.rep.fa以及hq_isoforms.fasta.no5merge.collapsed.gtf等文件,在进行去冗余的时候,阈值设置的高一些,因为三代就是对应的基因组的物种,所以设置-c 0.95以及-i 0.99 2 gffcompare合并 使用gffcompare软件将基因组注释和三代注释合并起来 gffcompare ref....
经过这一步的运行,可以得到hq_isoforms.fasta.no5merge.collapsed.rep.fa以及hq_isoforms.fasta.no5merge.collapsed.gtf等文件,在进行去冗余的时候,阈值设置的高一些,因为三代就是对应的基因组的物种,所以设置-c 0.95以及-i 0.99 2 gffcompare合并 使用gffcompare软件将基因组注释和三代注释合并起来 ...
(args.gff,':memory:',force=True,keep_order=True,merge_strategy="create_unique",sort_attribute_values=True)mRNA_children=("five_prime_UTR","three_prime_UTR","CDS","exon")idmap={"CDS":"cds","exon":"exon","five_prime_UTR":"5utrp","three_prime_UTR":"3utrp"}f_out=open('%s....
GallVp added this pull request to the merge queue Mar 19, 2024 View details Merged via the queue into nf-core:master with commit 5ed10bd Mar 19, 2024 11 checks passed GallVp deleted the gt/gff3validator branch March 19, 2024 23:06 vlebars pushed a commit to vlebars/modules tha...
-v turn on validation -r turn on replacement of escaped characters -f merge records into features -c N feature cache size (how many features to keep in memory), default=1000 -l link feature into parent-child relationships Before exiting, the utility prints the number of records or features...
git clone https://github.com/agshumate/Liftoff liftoff cd liftoff python setup.py install pip install Liftoff USAGE usage: liftoff [-h] (-g GFF | -db DB) [-o FILE] [-u FILE] [-exclude_partial] [-dir DIR] [-mm2_options =STR] [-a A] [-s S] [-d D] [-flank F] [-V] ...
#stringtie--merge-GF:\RNA-seq\algnment\sme.gff3-omerged.stringtie.gtfWT.cd1_1.fq_clean.fq.pos.sorted.assembly.gtfWT.cd2_1.fq_clean.fq.pos.sorted.assembly.gtfWT.unc1_1.fq_clean.fq.pos.sorted.assembly.gtfWT.unc2_1.fq_clean.fq.pos.sorted.assembly.gtf#StringTieversion2.1.4SMEL3Ch00.0...