SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 44
Search took 0.00 seconds.
Search: Posts Made By: foolishbrat
Forum: Bioinformatics 09-01-2017, 05:37 AM
Replies: 1
Views: 1,009
Posted By foolishbrat
Can or should we perform feature counting with `bedtools intersect -c`?

I have the following BAM file and a annotation file.
What I want to do is to calculate reads count in
I can do it with the following three methods.


Method1 bedtools intersect...
Forum: Bioinformatics 02-20-2017, 04:28 PM
Replies: 1
Views: 1,413
Posted By foolishbrat
Problem Converting BAM to SAM on to Amazon S3 Using Samtools

In my Amazon EC2 instance I have the following:


ubuntu@ip-133-31-16-230:~$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 79G 0 79G 0% /dev
tmpfs ...
Forum: Bioinformatics 02-11-2017, 03:35 AM
Replies: 4
Views: 2,540
Posted By foolishbrat
Hi Josh, Tried that. But still give low...

Hi Josh,

Tried that. But still give low mapping rate.

FB.
Forum: Bioinformatics 02-10-2017, 04:13 PM
Replies: 4
Views: 2,540
Posted By foolishbrat
Why mapping rate is low after adapter trimming paired-end data?

I have the pipeline with the following trimming and mapping parameter:



trim_galore --stringency 5 --dont_gzip --trim1 --length 30 -q 0 -a CTGTCTCTTATACACATCT -o $TRIMGALORE_DIR $READ1...
Forum: Bioinformatics 02-04-2014, 10:37 PM
Replies: 1
Views: 1,438
Posted By foolishbrat
Tools that report read count AND read names that map to genomic features.

htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) and coverageBed (http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html#s-calculating-coverage-by-strand) are...
Forum: Bioinformatics 01-30-2014, 04:47 AM
Replies: 1
Views: 1,311
Posted By foolishbrat
Meaning of blue cloud in meanSdPlot() of DESEq

The attached figure showed the meanSdPlot() from DESEq.

http://www.freeimagehosting.net/t/q1e55.jpg (http://www.freeimagehosting.net/)
What is the meaning of the bluish cloud at the background?...
Forum: Bioinformatics 01-29-2014, 04:28 AM
Replies: 1
Views: 1,494
Posted By foolishbrat
Obtaining genomic features from miRNA-seq data based on UCSC hg19 alignment results

I have miRNA-seq data (single end) which I map to the whole UCSC hg19 genome. Now given the SAM output of this mapping, what's the good pipeline to summarize that alignment so that I can get...
Forum: Bioinformatics 01-29-2014, 04:06 AM
Replies: 4
Views: 2,309
Posted By foolishbrat
Thanks a million.

Thanks a million.
Forum: Bioinformatics 01-29-2014, 01:02 AM
Replies: 4
Views: 2,309
Posted By foolishbrat
Thanks, two more questions: So if I remove...

Thanks, two more questions:

So if I remove -k1 that means for each read it will output only 1 best position, which doesn't mean it's uniquely mapped, am I right?

If so how can I determine the...
Forum: Bioinformatics 01-29-2014, 12:04 AM
Replies: 4
Views: 2,309
Posted By foolishbrat
Meaning of Negative Alignment Score in BOWTIE2 output

I have a mIRNA seq data in which I aligned it to whole genome UCSC hg19.
For that I use bowtie2 with the following parameter:

bowtie2 -x myindex -U my_mirna_seq.fastq --n-ceil L,0,0 -k 1 -N 1 ...
Forum: Bioinformatics 01-28-2014, 03:27 PM
Replies: 3
Views: 1,488
Posted By foolishbrat
Thanks a million both.

Thanks a million both.
Forum: Bioinformatics 01-27-2014, 04:12 AM
Replies: 3
Views: 1,488
Posted By foolishbrat
How to measure miRNA expression from Illumina libraries

I have a 51 single-end reads generated with MiSeq using NEBNext Multiplex Oligos for Illumina.

The data is obtained from from blood serum miRNA.

The sample sheet looks like this:
...
Forum: Bioinformatics 01-27-2014, 01:06 AM
Replies: 8
Views: 7,365
Posted By foolishbrat
Thank you.

Thank you.
Forum: Bioinformatics 01-27-2014, 12:45 AM
Replies: 8
Views: 7,365
Posted By foolishbrat
You save my life. If you don't mind one last...

You save my life. If you don't mind one last question.
How can I know whether or not to use the reverse complement adapter for trimming?

Any other alternative than GATC-s-T ending?
Forum: Bioinformatics 01-27-2014, 12:32 AM
Replies: 8
Views: 7,365
Posted By foolishbrat
Thanks a million! So in the trimming process,...

Thanks a million!
So in the trimming process, I don't have to care about the index sequence "GCCTAA" or it's reverse complement "TTAGGC". Am I right?
Forum: Bioinformatics 01-27-2014, 12:21 AM
Replies: 8
Views: 7,365
Posted By foolishbrat
Hi, Thanks. But the reverse complement of ...

Hi, Thanks.

But the reverse complement of

5 ́-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3 ́

Is this:...
Forum: Bioinformatics 01-26-2014, 09:45 PM
Replies: 8
Views: 7,365
Posted By foolishbrat
Adapter trimming NEBNext Library / MiSeq

I have a 51 single-end reads generated with MiSeq using NEBNext Multiplex Oligos for Illumina.

The sample sheet looks like this:

IEMFileVersion,4
Investigator Name,FB
Experiment...
Forum: Illumina/Solexa 01-26-2014, 09:30 PM
Replies: 1
Views: 3,683
Posted By foolishbrat
Best way to trim MiSeq - NEBNext Multiplex Oligos for Illumina Library

I have a 51 single-end reads generated with MiSeq using NEBNext Multiplex Oligos for Illumina.

The sample sheet looks like this:

IEMFileVersion,4
Investigator Name,FB
Experiment...
Forum: Bioinformatics 01-15-2014, 02:19 AM
Replies: 0
Views: 1,249
Posted By foolishbrat
How to extract split-reads from Pindel output

Is there a way to do it?
I couldn't make sense how to find the split-reads an its header from
the output.

Example output can be found here:

...
Forum: Helicos / Direct Genomics 09-07-2011, 02:43 PM
Replies: 3
Views: 6,401
Posted By foolishbrat
Yes, but they are all in FASTQ format. I want...

Yes, but they are all in FASTQ format.
I want to look at the raw output before conversion to FASTQ.
Forum: Helicos / Direct Genomics 09-07-2011, 04:59 AM
Replies: 3
Views: 6,401
Posted By foolishbrat
Sample Output of Helicos Raw Data

Hi all,

Where can I find sample output of Helicos Raw Data?
Does it have quality score?
Forum: General 05-31-2011, 07:19 PM
Replies: 2
Views: 1,874
Posted By foolishbrat
Counting Reads in SAM Format

Typically mapping output will show many reads that are very close to each other. Meaning the difference of mapping location differ within 10 positions.

Is there any existing tool to cluster such...
Forum: Illumina/Solexa 10-05-2009, 01:54 AM
Replies: 0
Views: 1,679
Posted By foolishbrat
SNP Database with Solexa/Illumina Reads

Is there any database where we can find Solexa/Illumina libraries
used for creating SNP database (e.g. Human SNP)?

The library can be in FASTQ format or standard Solexa output.
Forum: Bioinformatics 08-11-2009, 06:13 AM
Replies: 24
Views: 15,074
Posted By foolishbrat
Is there a way I can download "sffinfo". I tried...

Is there a way I can download "sffinfo". I tried to search google but of no avail.
Forum: Bioinformatics 08-10-2009, 07:15 PM
Replies: 0
Views: 1,819
Posted By foolishbrat
Error Probability of 454's Flowgram

Is there any resource where I can download the data
about the "error probability/error bar" of the flowgram?


Flowgram: 0.04 0.06 1.02 1.08 0.06 ....
Flow Indexes: 3 ...
Showing results 1 to 25 of 44

 


All times are GMT -8. The time now is 06:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO