User: bharata1803

gravatar for bharata1803
bharata1803420
Reputation:
420
Status:
Trusted
Location:
Japan
Last seen:
5 days, 19 hours ago
Joined:
4 years, 2 months ago
Email:
b**********@gmail.com

Posts by bharata1803

<prev • 231 results • page 1 of 24 • next >
2
votes
2
answers
100
views
2
answers
Answer: A: DEG from BAM file
... To do DEG analysis, what you need is a readcount table. So, you just need read count software that accept BAM files. Try HTSeq count or featureCount. After you get read count table, you can do DEG using popular library like DESeq2, EdgeR, or limma/voom. ...
written 6 days ago by bharata1803420
0
votes
0
answers
90
views
0
answers
Differential expression analysis for time course data
... Hello, I want to ask regarding time course data. The data I want to analyse is from human iPSC cell reprogramming with time course data from mature cell induce with Yamanaka factor to become iPSC with several time steps. What are the best ways to do this? Firstly, I am thinking to use CPM as a me ...
deseq2 rna-seq written 7 days ago by bharata1803420
0
votes
0
answers
137
views
0
answers
Comment: C: Getting raw FASTQ file from GDC/TCGA database
... well, I need the raw data because I want to use transcript level gene expression for my method. Unfortunately, GDC only has gene level expression result. So, I think having raw data myself, I could get the transcript level expression by myself. Currently I use data from NCBI GEO because there are m ...
written 29 days ago by bharata1803420
0
votes
0
answers
137
views
0
answers
Getting raw FASTQ file from GDC/TCGA database
... Hello, I just want to know whether we can obtain raw data from GDC/TCGA database. I heard they require you to submit some request but I don't know how to do it. I am a student so my credentials is very limited. Maybe I can ask my Professor to submit it if needed. Also does it takes long time for th ...
next-gen rna-seq written 4 weeks ago by bharata1803420 • updated 19 days ago by Biostar ♦♦ 20
0
votes
0
answers
87
views
0
answers
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 8 weeks ago by bharata1803420
0
votes
0
answers
207
views
0
answers
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 3 months ago by bharata1803420
0
votes
0
answers
207
views
0
answers
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 3 months ago by bharata1803420 • updated 28 days ago by Biostar ♦♦ 20
0
votes
1
answer
341
views
1
answers
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 3 months ago by bharata1803420
0
votes
1
answer
341
views
1
answers
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 3 months ago by bharata1803420
0
votes
1
answer
341
views
1
answers
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 3 months ago by bharata1803420

Latest awards to bharata1803

Popular Question 29 days ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Popular Question 3 months ago, created a question with more than 1,000 views. For Aligning TF binding site to target gene method
Student 3 months ago, asked a question with at least 3 up-votes. For Download human 3 UTR FASTA file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Dataset kind of data NCBI
Scholar 4 months 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
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Couldn't able to run the DESeq2
Popular Question 6 months ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
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 Microarray and RNA-seq different result
Popular Question 8 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 8 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 8 months ago, created a question with more than 1,000 views. For Detecting miRNA effect from RNA-seq
Popular Question 12 months ago, created a question with more than 1,000 views. For Alternative sequence gene Ensembl ID
Popular Question 12 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1237 users visited in the last hour