User: drkousi31

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drkousi310
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Posts by drkousi31

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Comment: C: Ambiguous reads in htseq-count
... Using `grep -v 'tRNA'` removes mRNA of genes like tRNA methyltransferase. Using `awk '$3 !~ /tRNA/'` retains exons of tRNA. Please check if this approach is correct. write lines without 'gene' `grep -v gene my.gff > no_gene_gff` Check features of no_gene_gff `awk '{print $3}' no_gene_gf ...
written 20 hours ago by drkousi310
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Comment: C: Ambiguous reads in htseq-count
... Sorry. Please help me how to filter tRNA lines? As the 3rd column has 3 features: gene, tRNA and exon. gbkey has variation between gene and tRNA. Some lines have gene_biotype=tRNA and some lines have product=tRNA instead. In some cases like in tRNA-methyltransferase gene, gbkey=mRNA and product= ...
written 1 day ago by drkousi310
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Comment: C: Ambiguous reads in htseq-count
... I downloaded gff file from ncbi with this [link][1] [1]: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/121/395/GCF_003121395.1_UOA_WB_1/GCF_003121395.1_UOA_WB_1_genomic.gff.gz Yes I am not interested in tRNAs. Should I filter all tRNAs or only the lines without 'gene' ? ...
written 1 day ago by drkousi310
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Comment: C: Ambiguous reads in htseq-count
... I tried with -i gene and got this error 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. . . . 1600000 GFF lines processed. Error occured when processing GFF file (line 1688729 of file /DATA/kous/g_index/GCF_003121395.1_UOA_WB_1_genomic.gff): Feature id83634 ...
written 1 day ago by drkousi310
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Comment: C: Ambiguous reads in htseq-count
... Thank you for pointing out the mistake in assigning the gene tag in "-i". The output I got is by using "-i ID", if you see my command above. As per the manual: If the name of the attribute containing the gene ID for exon lines is not gene_id, use the --idattr. Often, its is, for example, Parent, Ge ...
written 12 days ago by drkousi310
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Ambiguous reads in htseq-count
... Hi all, I have a dount in htseq-count output. I used samtools to extract uniquely mapped properly paired reads and sorted by name using the command samtools view -bS -h -q 40 -f 2 -F 512 ${i} | samtools sort -n -o ${i}_sorted.bam -@ 20 I used this output for htseq-count using the coomand ...
htseq-count rna-seq written 13 days ago by drkousi310
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Comment: C: which feature type and id attribute to use in ht-seq count
... According to the manual - https://htseq.readthedocs.io/en/release_0.11.1/count.html, by default it counts exon when aGTF file is provided. (-t , --type= feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an E ...
written 16 days ago by drkousi310
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which feature type and id attribute to use in ht-seq count
... Hi all I want to use ht-seq count for counting reads. I am planning to do both read counts for exons and gene, and compare them later. If I have understood right, we calculate exon counts to find differential expression between alternatively spliced transcripts which may not be visible in gene co ...
rna-seq written 16 days ago by drkousi310
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Comment: C: How to extract fasta sequence of lncRNA from whole ncRNA fasta of ucsc ftp downl
... I downloaded from wget https://raw.githubusercontent.com/santiagosnchez/faSomeRecords/master/faSomeRecords.py ...
written 21 days ago by drkousi310
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Answer: A: How to extract fasta sequence of lncRNA from whole ncRNA fasta of ucsc ftp downl
... Thank you. I directed grep 'lncRNA' output to headers.txt and used faSomeRecords.py. Bedtools would have been easier too, but I was not sure which option to use in 'Create one BED record per:' in table browser. FaSomeRecords.py worked good. ...
written 21 days ago by drkousi310

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