User: sg197

gravatar for sg197
sg19710
Reputation:
10
Status:
New User
Location:
Last seen:
3 days, 21 hours ago
Joined:
2 years, 4 months ago
Email:
s**********@yahoo.co.uk

Posts by sg197

<prev • 14 results • page 1 of 2 • next >
0
votes
0
answers
64
views
0
answers
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 8 days ago by sg19710
0
votes
0
answers
64
views
0
answers
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 8 days ago by sg19710
0
votes
0
answers
43
views
0
answers
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 11 days ago by sg19710
0
votes
0
answers
404
views
0
answers
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 7 months ago by sg19710
0
votes
0
answers
404
views
0
answers
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 7 months ago by sg19710
0
votes
0
answers
404
views
0
answers
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 7 months ago by sg19710 • updated 7 months ago by RamRS27k
0
votes
1
answer
285
views
1
answers
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 8 months ago by sg19710
0
votes
1
answer
285
views
1
answer
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 8 months ago by sg19710 • updated 8 months ago by Amar670
0
votes
2
answers
348
views
2
answers
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 months ago by sg19710 • updated 4 months ago by UVDorian0
0
votes
1
answer
985
views
1
answers
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 9 months ago by sg19710

Latest awards to sg197

Popular Question 6 months ago, created a question with more than 1,000 views. For How do I download mm10 major release genomic fasta and gtf file?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1518 users visited in the last hour