User: ilovesuperheroes1993
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Posts by ilovesuperheroes1993
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... 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
ilovesuperheroes1993 • 0
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... 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 ...
written 8 months ago by
ilovesuperheroes1993 • 0
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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
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 9 months ago by
ilovesuperheroes1993 • 0
• updated
9 months ago by
Grinch • 80
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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 9 months ago by
ilovesuperheroes1993 • 0
• updated
9 months ago by
michael.ante • 3.6k
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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 10 months ago by
ilovesuperheroes1993 • 0
• updated
10 months ago by
ATpoint ♦ 35k
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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 12 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 15 months ago by
ilovesuperheroes1993 • 0
• updated
15 months ago by
genomax ♦ 83k
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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 16 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 16 months ago by
ilovesuperheroes1993 • 0
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