User: ilovesuperheroes1993

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Posts by ilovesuperheroes1993

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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 26 days 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 26 days ago by ilovesuperheroes19930 • updated 26 days ago by Grinch70
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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 5 weeks ago by ilovesuperheroes19930 • updated 5 weeks ago by michael.ante3.4k
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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 6 weeks ago by ilovesuperheroes19930 • updated 6 weeks ago by ATpoint22k
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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 3 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 7 months ago by ilovesuperheroes19930 • updated 7 months ago by genomax71k
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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 7 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 7 months ago by ilovesuperheroes19930
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Find the 3' utrs, 5'utrs and their counts from bam files
... Hello, I have bam files of 8 samples (4 normal and 4 diseased), produced by alignment with novoalign (small-rna sequencing data). I have excluded the mirna from the bam files by using the following command: bedtools intersect -v "sample.bam" "hg19_mirna.gff3" > output.bam In this manner I ...
bedtools bed bam utr ucsc written 7 months ago by ilovesuperheroes19930 • updated 7 months ago by Gautier Richard280

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