User: silas008

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silas00880
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Brazil
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Posts by silas008

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Comment: C: Bowtie2 mapped just 50% of the reads
... In general contamination, as rRNA, have millions of reads overexpressed. I have checked the overexpressed reads in fastqc and they are miRNA reads. Do you think should I use a specific program for that? Thanks ...
written 4 weeks ago by silas00880
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Comment: C: Bowtie2 mapped just 50% of the reads
... It is a good point. I will try it again with Bowtie1 to see what happen. Thanks ...
written 4 weeks ago by silas00880
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Comment: C: Bowtie2 mapped just 50% of the reads
... I think this is not the problem because STAR aligner have mapped more than 90% of the reads. Another point is that I think I mapped this data about 1 year ago using Bowtie2.2.7 instead of the last release and it also worked well. ...
written 4 weeks ago by silas00880
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Bowtie2 mapped just 50% of the reads
... Hey, guys. I need some help with Bowtie2. It will be great if you can help me. I am trying to align small RNA seq data to C elegans genome. The pre-processing is ok (good base quality, no adapters, reads are trimmed and etc). But in the alignment step bowtie2 only aligned about 50% of all reads. Th ...
rna-seq written 4 weeks ago by silas00880 • updated 14 days ago by Biostar ♦♦ 20
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Comment: C: How to extract reads from bam file?
... I really didn't know why this was not working. I will try your suggestion. Thanks ...
written 6 months ago by silas00880
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Comment: C: How to extract reads from bam file?
... Now i am using -L option and a bed file and the **output.bam** is ok. There are a lot of reads. Thanks ...
written 6 months ago by silas00880
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Comment: C: How to extract reads from bam file?
... I will do that. Thanks again ...
written 6 months ago by silas00880
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Comment: C: How to extract reads from bam file?
... First of all, thank you for helpping. I am sorry for the formatting, I am not so familiar with Biostars. I didn't know there is a code formatting bar. I will use it in next posts. I am using Samtools version 1.4 and the option -L worked very well for me. I didn't know what I was doing wrong before ...
written 6 months ago by silas00880
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How to extract reads from bam file?
... Hi, guys! I am trying to extract some reads that aligned in specific regions of the mitochondrial genome. I want to know what is the length of these reads, so I need to extract them before to measure, to avoid the measurement of other reads the aligned in other regions. I did it by different ways, ...
alignment rna-seq written 6 months ago by silas00880 • updated 6 months ago by RamRS20k
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Comment: C: PCA plot from read count matrix from RNA-Seq
... How can I put the names of the samples in this case? And different colors for it group? Because in the pipeline there are just the basic information to plot a simple graph. Tks ...
written 6 months ago by silas00880

Latest awards to silas008

Popular Question 6 months ago, created a question with more than 1,000 views. For GEO (NCBI) confusing data
Popular Question 6 months ago, created a question with more than 1,000 views. For GFF3 to GTF
Great Question 7 months ago, created a question with more than 5,000 views. For LogFC and LogCPM
Supporter 7 months ago, voted at least 25 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For GFF3 to GTF
Popular Question 21 months ago, created a question with more than 1,000 views. For Problem with Fastqc quality control for miRNAseq data
Popular Question 21 months ago, created a question with more than 1,000 views. For I need to know how to trimming RNAseq of GEO dataset.
Popular Question 21 months ago, created a question with more than 1,000 views. For How to save a terminal output in a txt file?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For GFF3 to GTF
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Problem with trimming ilumina adapter

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