Question: how can I analysis data from ebi.uk
0
gravatar for Learner
9 months ago by
Learner 100
Learner 100 wrote:

I would like to know two things

1- why when I look at the ebi.uk for a sample, the fastq files are split in two part for each sample?

2- how to identify if a data is single end or paird reads?for example, I only know Illumina HiSeq 2000 (Homo sapiens). Is there a way to know that?

3- how to know if a the fastq is forward reads or reverse reads and why one should generate that?

thanks

rna-seq • 332 views
ADD COMMENTlink modified 9 months ago by Kritika260 • written 9 months ago by Learner 100
2
  1. You said two things. There are 3.
  2. What have you tried? Have you searched online? Have you read any book?
ADD REPLYlink written 9 months ago by RamRS19k

@Ram answering my question by a question :-) do you think that if I knew the answer I would ask here it? I have been searching like a crazy, I have been trying to find a solution for it for a day but I could not find anything. If you know a source i would appreciate to direct me or simply tell me what it is thanks

ADD REPLYlink written 9 months ago by Learner 100

That is not how learning works. In a scientific forum, you have to tell us what kind of effort you've put in. The reason I ask "what have you tried" is because these are common questions, and I know that if you'd tried searching, you'd find answers with minimal effort.

ADD REPLYlink written 9 months ago by RamRS19k
3
gravatar for Kritika
9 months ago by
Kritika260
India
Kritika260 wrote:

1- why when I look at the ebi.uk for a sample, the fastq files are split in two part for each sample?

A :- These are two pairend reads of one sample that is forward read and reverse reads

2- how to identify if a data is single end or paird reads?

A:- if you have two reads designated for example sample1_1 and sample1_2 or cell1_1 and cell1_2 then its a pairend reads if this is one than its a single end reads

3- how to know if a the fastq is forward reads or reverse reads and why one should generate that?

A:-While downloading fastq file look lines which starts with @ this line has information 1 or 2 in the end of this lines so 1 then its reverse if it 2 then its forward

ADD COMMENTlink modified 9 months ago • written 9 months ago by Kritika260
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