User: sg197

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sg19710
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Posts by sg197

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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 24 days ago by sg19710
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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 24 days ago by sg19710
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StringTie error input file not sorted, even though it is
... I've been following [the stringtie pipeline for differential expression](http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual). I'm up to the stage of `stringtie -e -B` where I'm using the merged transcript file with the alignment (.bam) files to get read coverage tables. root="/mnt/fls01 ...
stringtie rna-seq written 26 days ago by sg19710 • updated 26 days ago by RamRS25k
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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 6 weeks ago by sg19710
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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 6 weeks ago by sg19710 • updated 6 weeks ago by Amar620
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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 9 weeks ago by sg19710 • updated 9 weeks ago by Kevin Blighe52k
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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 10 weeks ago by sg19710
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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 10 weeks ago by sg19710 • updated 10 weeks ago by h.mon29k
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Are single-end reads processed the same as paired-end reads regarding strandedness?
... I have RNA-seq data made from Illumina TruSeq Stranded mRNA Sample Preparation Kit. Some of my samples are paired end, however one set is single end. I have already processed the paired end ones, and understand to use 'reverse-strand' or -s 2 for featureCounts. Do I do the same for single end read ...
featurecounts strandedness single-end rna-seq written 10 weeks ago by sg19710 • updated 10 weeks ago by ATpoint26k
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Comment: C: How do I download mm10 major release genomic fasta and gtf file?
... Thanks, I hadn't come across the gencode website before! ...
written 10 weeks ago by sg19710

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