User: sg197

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sg19720
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Posts by sg197

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Comment: C: find co-ordinates of overlapping fasta sequences
... If I understand what you're suggesting, I already have the 'overlapping part', that's my fasta file of the mature microRNA. It's the overlapping wrt to genome that I'm having trouble with... as these are short reads I think they may align to multiple places and not just within the precursor region ( ...
written 4 months ago by sg19720
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find co-ordinates of overlapping fasta sequences
... Hi, I have 2 fasta files (one of precursor novel microRNAs and one of mature novel microRNAs), and a bed file of the precursors. What I want to do is find where the 2 fasta files overlap and get the coordinates, relative to the precursor bed. I can't find any tool that would let me do this... the cl ...
bedtools fasta micrornas written 4 months ago by sg19720
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miRDeep2 sample read count different between mapper.pl and quantifier.pl
... Hi, I'm using miRDeep2 for novel microRNA prediction and also counting reads for both novel and known microRNAs. After using mapper.pl, I get this output: #desc total mapped unmapped %mapped %unmapped S01: 24882381 22106271 2776110 88.843 11.157 S02: 30468230 26078475 4389755 85.592 14 ...
mirdeep2 rna-seq microrna written 4 months ago by sg19720
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Comment: C: StringTie error input file not sorted, even though it is
... Just realised it's an issue with the reading in the file, not the file itself. Thanks for the suggestions anyway! ...
written 11 months ago by sg19720
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Comment: C: StringTie error input file not sorted, even though it is
... Hi, I sorted the bam files using STAR output settings (used instead of HISAT). I've checked the bam file using `samtools view -H $file | grep s0` and the output returned `@HD VN:1.4 . s0:coordinate` so it is definitely sorted. The gtf file is also sorted in the same order, chr1 onwards, so it can't ...
written 11 months ago by sg19720
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Comment: C: Using StringTie output GTF with featureCounts to assign reads- low assigned perc
... Thanks for the suggestion, I tried it and using that output gtf it gave me the original assigned percentage with featurecounts. But I read in the manual that -e option causes reads with no reference transcript to be skipped, so I think this is missing out any novel transcripts? manual description: L ...
written 12 months ago by sg19720
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Using StringTie output GTF with featureCounts to assign reads- low assigned percentage
... Hi, I originally used featurecounts to assign reads to known transcripts of the mm10 genome. The percentage of fragments assigned was between 70-75% for my samples. Using this original gtf file the number of features (exons) were 841916, and meta-features (genes) were 55421. I since came across S ...
stringtie featurecounts rna-seq written 12 months ago by sg19720 • updated 12 months ago by Mark800
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R AnnotationDbi returning NA for pseudogenes during gene id annotation
... I'm using "AnnotationDbi" and "org.Mm.eg.db" in R to annotate gene ids of DE genes with both their gene symbol and entrez id. My original gtf file was downloaded from ensembl, so I'm using ensembl as the keytype. For some of the genes it works, however for many instead of a symbol and ID it returns ...
annotationdbi R deseq2 pseudogene ensembl written 12 months ago by sg19720 • updated 8 months ago by UVDorian0
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Comment: C: Difference between read counts STAR vs featureCounts
... Ok if I understand right then featureCounts is counting multi mapped fragments each as unique fragments (with different genomic co-ords) even though they are the same original read-pair? Would you recommend leaving the STAR default as 10 for aligning to the genome? On a side note I've also been rea ...
written 13 months ago by sg19720
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Difference between read counts STAR vs featureCounts
... I aligned some paired-end RNA-seq data using STAR and then used featureCounts on the output .bam to assign them to genes. However I'm really confused as the output of featureCounts shows that I have more fragments (read-pairs) than the number of total input reads (I'm assuming also read-pairs/fragme ...
featurecounts star rna-seq multimapped written 13 months ago by sg19720 • updated 13 months ago by h.mon31k

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Popular Question 10 months ago, created a question with more than 1,000 views. For How do I download mm10 major release genomic fasta and gtf file?

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