User: ilovesuperheroes1993
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Posts by ilovesuperheroes1993
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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
ilovesuperheroes1993 • 0
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... 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 ...
written 26 days ago by
ilovesuperheroes1993 • 0
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26 days ago by
Grinch • 70
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... 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 ...
written 5 weeks ago by
ilovesuperheroes1993 • 0
• updated
5 weeks ago by
michael.ante • 3.4k
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... 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 ...
written 6 weeks ago by
ilovesuperheroes1993 • 0
• updated
6 weeks ago by
ATpoint ♦ 22k
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... 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 ...
written 3 months ago by
ilovesuperheroes1993 • 0
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... 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 ...
written 7 months ago by
ilovesuperheroes1993 • 0
• updated
7 months ago by
genomax ♦ 71k
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... 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
ilovesuperheroes1993 • 0
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... 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
ilovesuperheroes1993 • 0
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... 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 ...
written 7 months ago by
ilovesuperheroes1993 • 0
• updated
7 months ago by
Gautier Richard • 280
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