User: bharata1803

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bharata1803390
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Japan
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Posts by bharata1803

<prev • 227 results • page 1 of 23 • next >
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FIMO parameter for PWM motif scanning
... Hello, I have several questions regarding the use of FIMO as motif scanning. I have used it for a while but I still don't understand some part of it. 1. Regarding low complexity region or repeating region. I noticed that FIMO result actually match a lot with repeating region. Does this mean anythi ...
fimo pwm written 2 days ago by bharata1803390
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Comment: C: Subread and featurecounts read index and annotation once for all
... Usually I use salmon, but this time the fastq is colorspace. So, I need to use aligner that support colorspace which is subread. I am used to use salmon with fast process and now stuck in subread with 30 minutes per file processing. ...
written 5 weeks ago by bharata1803390
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Subread and featurecounts read index and annotation once for all
... Hello, I noticed that subread aligner and featurecounts software both loading the index and annotation at the beginning. If I want to process multiple fastq and bam, is it possible to process it at once? Loading the index itself take several minutes so if there are any methods to bulk align and bul ...
alignment featurecounts rna-seq written 5 weeks ago by bharata1803390
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Comment: C: FASTQ alignment result is really bad
... I realized I aligned it to cdna/transcript reference, not whole genome reference. I aligned to cdna reference because I wanted try to count the reads with salmon. I will try to align it to the genome then. ...
written 5 weeks ago by bharata1803390
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Comment: C: FASTQ alignment result is really bad
... Thanks, I will try your method. I have tried subread but I got 20% mapped reads which is quite bad. If I can get 60% like you probably the data can be used. ...
written 5 weeks ago by bharata1803390
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Comment: C: FASTQ alignment result is really bad
... I gave up with this dataset, the fastq quality seems really bad. I have checked their processed data too and try to use DESeq2 to get the differential expression. The result is bad too with only small number of genes are giving siginificant result. ...
written 5 weeks ago by bharata1803390
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Comment: C: FASTQ alignment result is really bad
... It is a bit hard to check the quality because FastQC cannot be used for colorspace. Is there any fastq quality control software that can handle the colorspace data? If you got 65% reads, I think it is good enough. I will try using subread. Do you mind posting you command with subread so that I can r ...
written 5 weeks ago by bharata1803390
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Comment: C: FASTQ alignment result is really bad
... It is in colorspace. I have checked it. I will post the head result later. ...
written 5 weeks ago by bharata1803390
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Comment: C: FASTQ alignment result is really bad
... I am still confused. I have tried using bowtie to make colorspace index and align in colorspace, but it is still almost 0% reads that can be mapped to the reference. It is really weird. ...
written 5 weeks ago by bharata1803390
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Comment: C: FASTQ alignment result is really bad
... I will try bowtie. It seems bowtie support colorspace ...
written 5 weeks ago by bharata1803390

Latest awards to bharata1803

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Student 6 weeks ago, asked a question with at least 3 up-votes. For Download human 3 UTR FASTA file
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Couldn't able to run the DESeq2
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to visualize a set of sequence alignments that all have the same reference s
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Dataset kind of data NCBI
Popular Question 4 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 4 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 4 months ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 4 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 6 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 6 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 6 months ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 10 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 10 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 10 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file

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