User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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How to align the sanger sequenced fragments against human reference gene?
... Hi folks, I have been provided sequence file from Sanger sequencing platform. It has 12 exons, so the technician has captured 5'UTR+exon1, exon2, exon3,.......exon12+3'UTR. He asked me to align with the human reference gene and try to find the variants from it. He provided me many fragments of sequ ...
dnaseq alignment align sanger written 5 days ago by bioinforesearchquestions140 • updated 4 days ago by WouterDeCoster29k
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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 9 weeks ago by bioinforesearchquestions140
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Comment: C: Need help in selecting the correct output file from miRDeep2?
... Thanks, I have made changes to the existing post itself. ...
written 9 weeks ago by bioinforesearchquestions140
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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 9 weeks ago by bioinforesearchquestions140
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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 9 weeks ago by bioinforesearchquestions140
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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 9 weeks ago by bioinforesearchquestions140
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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 10 weeks ago by bioinforesearchquestions140
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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 10 weeks ago by bioinforesearchquestions140
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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 3 months ago by bioinforesearchquestions140
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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 4 months ago by bioinforesearchquestions140

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