User: bioinforesearchquestions

Reputation:
120
Status:
Trusted
Location:
United States
Last seen:
15 hours ago
Joined:
2 years, 6 months ago
Email:
b***********************@gmail.com

Posts by bioinforesearchquestions

<prev • 212 results • page 1 of 22 • next >
0
votes
0
answers
47
views
0
answers
While generating the % of mapped reads to all miRNAs, do I need to consider unique or multi-match reads?
... Hi folks, I am trying to create a table for the distribution of mapped RNA sequenced reads across miRBase v.21 for each isomiRs. I am using contents from this **miRBase.mrd** file to generate the reads mapped to isomiRs. I have copied the sample output from **miRBase.mrd** file generated using m ...
rnaseq mirdeep2 mirna written 16 hours ago by bioinforesearchquestions120
0
votes
0
answers
159
views
0
answers
Comment: C: Need help in selecting the correct output file from miRDeep2?
... Thanks, I have made changes to the existing post itself. ...
written 22 hours ago by bioinforesearchquestions120
0
votes
0
answers
21
views
0
answers
Comment: C: Need help in selecting the correct output file from miRDeep2?
... Hi Michael, I am going to delete the old one and retain the new one. ...
written 23 hours ago by bioinforesearchquestions120
0
votes
1
answer
1.6k
views
1
answers
Comment: C: How to anntate small-RNA seq reads distribution
... Hi, I am planning to do the same requirement as yours. Annotate the percent of reads with miRNA, snoRNA, rRNA, tRNA and repeat for sequenced reads from pig. Would you provide any recommendations? ...
written 4 days ago by bioinforesearchquestions120
1
vote
0
answers
71
views
0
answers
how to annotate (rRNA, tRNA, Mt_rRNA, Mt_tRNA, etc) sequenced small RNA reads
... Hi, I have small RNA sequenced data. I annotated the small RNA sequenced reads against miRBase for miRNAs. I would like to annotate the sequenced small RNA reads into the following mRNA_coding_sequence rRNA tRNA mRNA_1000 TSS + 5UTR mRNA_3UTR Mt_rRNA Mt_tRNA misc_RNA piRNA snRNA snoRNA ...
annotation small rna rna-seq written 4 days ago by bioinforesearchquestions120
0
votes
0
answers
74
views
0
answers
Comment: C: What are the methods to downsample the Depth of coverage (ex: 50X -> 25X)?
... readCounter is present inside the HMMcopy/scripts directory. Thanks, I fixed it. I removed the -b parameter, it was creating the index. Without the -b parameter I got the wiggle file. But my query is -s 0.15 does it mean 15X or less than 15x? I am getting error with the BAM file when I tried compu ...
written 11 days ago by bioinforesearchquestions120
0
votes
0
answers
74
views
0
answers
What are the methods to downsample the Depth of coverage (ex: 50X -> 25X)?
... Hi folks, I used this option to downsample the bam files. Am I doing it correctly? samtools view -s 0.15 -b input.bam > input_15X.bam Then I used this input_15X.bam to generate wig file using HMMcopy. readCounter -b input_15X.bam > input_15X.wig Building index for input_15X.bam, please h ...
wig downsample bam depth written 12 days ago by bioinforesearchquestions120
0
votes
0
answers
159
views
0
answers
Need help in selecting the correct output file from miRDeep2?
... Hi friends, We sequenced miRNA from 12 pig samples. I did the analysis using miRDeep2 tool. My aim is to find isomiRs for each sample. I have written a perl script to annotate isomiRs for the reads mapped to miRNA . I get the below output. The My doubt is, am I using the correct output file for t ...
mirbase mirdeep2 rna-seq mirna written 6 weeks ago by bioinforesearchquestions120
0
votes
0
answers
118
views
0
answers
Which one do I need to consider single-read or multi-read mappability bigwig file for creating mouse mappability file?
... Hi, I am using HMMcopy to generate copy number alterations for my samples. I am trying to create mm9 or mm10 mappability wiggle file from mouse bigwig file. I found the below mappability files from this article "Mappability of the mouse and human genomes and methylomes with Umap and Bismap" I a ...
mouse mm10 mm9 mappability hmmcopy written 8 weeks ago by bioinforesearchquestions120
0
votes
1
answer
164
views
1
answers
Comment: C: How to create bigwig using mm10.fasta and mm10.fasta bowtie index files
... Hi Genomax, I reinstalled the tool it worked. ...
written 8 weeks ago by bioinforesearchquestions120

Latest awards to bioinforesearchquestions

Popular Question 3 months ago, created a question with more than 1,000 views. For How to visualize large VCF files
Popular Question 5 months ago, created a question with more than 1,000 views. For How to visualize large VCF files
Popular Question 5 months ago, created a question with more than 1,000 views. For How to visualize large VCF files
Popular Question 5 months ago, created a question with more than 1,000 views. For How to visualize large VCF files
Popular Question 10 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Popular Question 11 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Popular Question 12 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Popular Question 17 months ago, created a question with more than 1,000 views. For Applying hard filters for variants
Supporter 17 months ago, voted at least 25 times.
Centurion 17 months ago, created 100 posts.
Popular Question 18 months ago, created a question with more than 1,000 views. For Applying hard filters for variants

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 825 users visited in the last hour