User: ilovesuperheroes1993

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Posts by ilovesuperheroes1993

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Comment: C: How toconvert a set of motif consensus sequences in IUPAC to meme format?
... Yes there is the iupac2meme utility. iupac2meme Usage: iupac2meme [options] + It works fine if I type in a single motif sequence at a time. How do I use this for multiple motifs in one go? ...
written 4 weeks ago by ilovesuperheroes19930
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How toconvert a set of motif consensus sequences in IUPAC to meme format?
... I am trying to run FIMO from MEME Suite to to search for occurrences of a list of motifs in my DNA sequences. The list of motifs are present in IUPAC format, given by their consensus sequences. I have a text file containing the motif name followed by its consensus sequence or Sequence logo as given ...
fimo meme motif transfac meme suite written 4 weeks ago by ilovesuperheroes19930 • updated 29 days ago by shenwei3565.5k
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Comment: C: Ambiguous results of RNA-Seq data using stringtie with edgeR
... Yes I did transcript assembly with StringTie using the command mentioned above. This generated the gtf files for each sample which were used as inputs for converting the fpkms to raw counts using PrepDE.py. Was I required to do anything else in this step? The paired nature of the samples was known ...
written 3 months ago by ilovesuperheroes19930
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Ambiguous results of RNA-Seq data using stringtie with edgeR
... Hi, I have human RNA-Seq (Total RNA) data of 24 paired samples. My samples are labelled as S1,S2,S3 and so on. S1-S2 form a pair and S3-S4 for another (odd represents Normal samples and even diseased samples). I have used STAR to align the reads and have obtained an overall alignment of > 90% ...
stringtie rna-seq edger written 3 months ago by ilovesuperheroes19930 • updated 6 weeks ago by swbarnes28.9k
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Comment: C: Alternate Splicing Analysis using rMATS for paired samples
... I have found the answer. In the optional parameters there is the option --analysis Type P/U. It seems that the above option was available for rMATS 3.4. This option is not available for the latest version. Why is this so? ...
written 13 months ago by ilovesuperheroes19930
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Alternate Splicing Analysis using rMATS for paired samples
... I am using rMATS (version 4.0.2) to test for alternate splicing. I have 12 paired samples (12 replicates for normal and 12 replicates for diseased). Sample 1 (Normal) is paired with Sample 2 (Diseased) Sample 3 (Normal) is paired with Sample 4 (Diseased) ..and so on It is mentioned that rMATS can ...
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Comment: C: Distribution of mapped reads
... Yes it was done with the NEBNext small RNA kit, specifically for miRNA and piRNA ...
written 14 months ago by ilovesuperheroes19930
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Distribution of mapped reads
... Hi, I have the bam files of small RNA sequencing data mapped to the human reference genome by STAR. I have to find out the percentage of reads that mapped to: (1) miRNA (2) lncRNA (3) piRNA (4) other non-coding rna (5) introns (6) 3- and 5- utrs (7) promoters I started by finding out the reads ...
bedtools alignment small rnaseq rna-seq mirna written 14 months ago by ilovesuperheroes19930 • updated 14 months ago by Grinch90
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BAM File size increased after extracting unique reads
... Hi, I had used STAR aligner for mapping my reads, and the output BAM files were sorted by coordinate. I used the follwing command to extract unique reads from my bam files: samtools view -q 255 input_file.bam > unique_reads.bam (SAM Flag 255 corresponds to unique alignments in STAR) Howe ...
alignment samtools star bam uniuque mapping written 14 months ago by ilovesuperheroes19930 • updated 14 months ago by michael.ante3.6k
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Genome coverage within specified regions
... Hi, I have a bed file containing the coordinates of certain regions of the genome. I want to get the genome coverage of these regions at each base position (i,e, similar to using -d option in bedtools genomecov). example bed file chr1 100 200 chr5 250 300 I want the output in the following m ...
bedtools genomecov coverage written 15 months ago by ilovesuperheroes19930 • updated 15 months ago by ATpoint40k

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