User: ilovesuperheroes1993

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Posts by ilovesuperheroes1993

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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 8 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 9 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 9 months ago by ilovesuperheroes19930 • updated 9 months ago by Grinch80
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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 9 months ago by ilovesuperheroes19930 • updated 9 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 10 months ago by ilovesuperheroes19930 • updated 10 months ago by ATpoint35k
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FastQC Poor Quality in first base only
... I had sequenced a total of 39 microbium samples. Of these 37 are pure cultures, grown in the lab, and the remaining two were randomly obtained from soil. These samples were sequenced (paired-end sequencing of the 16s metagenome). In case of the pure samples, they all passed the quality checks in Fa ...
ngs fastqc base quality sequencing written 12 months ago by ilovesuperheroes19930
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Annotation file of piRNAs
... Hello, I am trying for some time to find the annotation file (gtf / gff3) of all the piRNAs of human (hg19) and mouse (mm10). ( I need hg19 and mm10 versions specifically as all my previous upstream analysis had been done using these versions) I have searched everywhere, but still unable ...
mm10 pirna ncrna gtf / gff3 hg19 written 15 months ago by ilovesuperheroes19930 • updated 15 months ago by genomax83k
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Comment: C: Find the 3' utrs, 5'utrs and their counts from bam files
... Hi, I am currently using hg19 database (Grch37 version). I am unable to find the gtf / gff3 files of the utrs of this version. Could you please link me to them? Thanks a lot ...
written 16 months ago by ilovesuperheroes19930
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Comment: C: Find the 3' utrs, 5'utrs and their counts from bam files
... Thank you. Actually I want to get a gtf file of the utr sequences, and then count the reads using htseq-count. But I am unable to find the gtf files of 3' and 5' utrs. Do you know where I could get it? ...
written 16 months ago by ilovesuperheroes19930

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