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User: yaghoub.amraei

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Posts by yaghoub.amraei

<prev • 27 results • page 1 of 3 • next >
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Comment: C: extract stem-loop fasta sequence
... thank you for comment ...
written 23 days ago by yaghoub.amraei • 10
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extract stem-loop fasta sequence
... Hello to all I have a series of Small RNA-seq data that was actually the output of the mapping reads Small RNA-seq with mirbase database by Genomic CLC software. Now I need to use the mapping output to get the sequences conseve using the accession number of the stem-loop structures on the mirbase da ...
next-gen rna-seq written 24 days ago by yaghoub.amraei • 10
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Comment: C: extract fasta sequence based on gene distance
... hello. amazing, as usual. ...
written 4 weeks ago by yaghoub.amraei • 10
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lncRNA detaction from output cuffcompare or cuffmerge
... Hello everyone .. My goal is to identify LncRNA in rice plants. In some articles, they have used the output of cuffcompare or cuffmerge. If we use the output of the cufffmerge, we can only use intergenic LncRNA with class_code (u) and LncRNA on the antisense string (Lnc-NATs) with class_code (x). Bu ...
assembly rna-seq written 4 weeks ago by yaghoub.amraei • 10
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Comment: C: extract fasta sequence based on gene distance
... my gold is LncRNA detection. The number of each line in the GTF file, of which I want to identify the LncRNA, is about 50,000 transcripts, and when I get the Festa file with GFF, I have about 17,000 transcripts. That is, GFFRID gives the Festa file based on a transcript, not based on the gene distan ...
written 4 weeks ago by yaghoub.amraei • 10
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extract fasta sequence based on gene distance
... Hello everyone ... I have a cuffcompare output that has the same genes names and transcripts names, but the gene distance of each transcript is different with the same name. How can I get the fastasequence of any genes distance with the Bad Tools or GFF Read package? 1 Cufflinks exon 58474 6119 ...
assembly sequence written 4 weeks ago by yaghoub.amraei • 10
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Comment: C: extract transcrips_id and gene_id from output cuffcampare
... hello. amazing, as usual. ...
written 4 weeks ago by yaghoub.amraei • 10
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Comment: C: extract transcrips_id and gene_id from output cuffcampare
... 1 Cufflinks exon 2899 3255 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Os01g0100100"; oId "CUFF.7.2"; nearest_ref "Os01t0100100-01"; class_code "j"; tss_id "TSS1"; 1 Cufflinks exon 3354 3616 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exo ...
written 4 weeks ago by yaghoub.amraei • 10
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extract transcrips_id and gene_id from output cuffcampare
... آHi all. I have a cuffcompare output and I want to extract the transcript_id andgene_id in column 9, which is a string, using grep or AWK. Thank you for your guidance 1 Cufflinks exon 2899 3255 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Os01g0100100 ...
assembly written 4 weeks ago by yaghoub.amraei • 10
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Comment: C: filtered tab delimited file with awk
... It was great .. Thank you ...
written 7 weeks ago by yaghoub.amraei • 10

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