User: eromasko

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eromasko120
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Posts by eromasko

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Consensus of multiple BED files
... Hi bruce.moran. I think the BEDtools [intersect][1] combined with the [groupby][2] command might be helpful here. **Groupby** > Collapsing: listing all of the values in the opCol for a given group.¶ > Now for something different. What if we wanted all of the names of the repeats listed on th ...
written 3.1 years ago by eromasko120
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Comment: C: Bedtools - writing to an output files results in empty files
... Hi Sadia. The `sort` command is a unix command, which you can do without having bedtools installed. Can you tell us a little bit more about the file that is created after doing the command and can you show us the first few lines of the input file that you are using? Thanks. ...
written 3.1 years ago by eromasko120
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Answer: A: DESeq2 analysis for multiple conditions
... In looking up 'results' in the DESeq2 manual at http://www.bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf , I find the following information which suggests that it is only doing the first and last condition comparison: > The results table when printed will provide the infor ...
written 4.4 years ago by eromasko120 • updated 13 hours ago by RamRS24k
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Comment: C: MEME: how to get figures of conserved motifs?
... I have some experience with doing some semi-large datasets and have used -maxsize up to 500000. It starts to get really computationally- and time-intensive. For example, I had datasets of almost 500 sequences that were each 1000nt long and it starts to drag on, especially when you start considering ...
written 4.4 years ago by eromasko120
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Comment: C: MEME: how to get figures of conserved motifs?
... Actually, I should have put E-value earlier instead of p-value, as that is what is returned. The significant cutoff is value is still less than 0.05. Here is a short description of the E-value in the HTML output of MEME (also, you can find more information within the manual on the link I posted earl ...
written 4.4 years ago by eromasko120
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Answer: A: MEME: how to get figures of conserved motifs?
... Hi biolab. If I remember correctly, for your command with no changes to -nmotifs, only 1 motif will be returned even if there is more than 1 significant identified motif. When you say the meme.txt output shows many motifs with very low p-values, are they less than 0.05? Also, I'm not sure what you m ...
written 4.4 years ago by eromasko120
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Comment: C: Unable to use biomaRt getSequence() query to get sequences using genomic coordin
... Hi Sean. I tried that and got this as the output: Please specify the type of sequence that needs to be retrieved when using biomaRt in web service mode. Choose either gene_exon, transcript_exon, transcript_exon_intron, gene_exon_intron, cdna, coding, coding_transcript_flank, coding_gene_flank, tran ...
written 4.6 years ago by eromasko120
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Comment: C: Unable to use biomaRt getSequence() query to get sequences using genomic coordin
... library("biomaRt") ensembl<-useMart("ensembl",dataset="mmusculus_gene_ensembl") filters<-listFilters(ensembl) attributes<-listAttributes(ensembl) geneIDs<-readLines(“/home/ed/RWD/germ_cell/TXT/IDs.txt”) chr<-readLines(“/home/ed/RWD/germ_cell/TXT/chr.txt”) startpos<-readLines(“/home ...
written 4.6 years ago by eromasko120
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Unable to use biomaRt getSequence() query to get sequences using genomic coordinates
... After trying to download sequences through biomaRt using the getSequence() query with MGI IDs with some problems of duplicate IDs (please see: https://www.biostars.org/p/133594/ for additional information), I am trying a different approach where I strictly use genomic coordinates of the sequences I ...
R biomart bioconductor written 4.6 years ago by eromasko120 • updated 4.6 years ago by Sean Davis25k
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Comment: C: biomaRt duplicates some unique IDs during getSequence() query but not others
... MGI:1915804 MGI:1916541 MGI:1922895 MGI:1922764 MGI:1917623 MGI:1922873 MGI:1920637 MGI:1920832 MGI:1923913 MGI:1913628 MGI:1920923 MGI:1919402 MGI:1913561 MGI:1913828 MGI:1919831 MGI:1914669 MGI:1917941 MGI:1921185 MGI:1922105 MGI:1918893 MGI:1921916 ...
written 4.6 years ago by eromasko120

Latest awards to eromasko

Scholar 2.3 years ago, created an answer that has been accepted. For A: DESeq2 analysis for multiple conditions
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Unable to use biomaRt getSequence() query to get sequences using genomic coordinates
Supporter 3.0 years ago, voted at least 25 times.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Consensus of multiple BED files
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Unable to use biomaRt getSequence() query to get sequences using genomic coordinates

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