SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 20 of 20
Search took 0.00 seconds.
Search: Posts Made By: krapulaxdoctor
Forum: Bioinformatics 01-12-2018, 09:06 AM
Replies: 2
Views: 1,216
Posted By krapulaxdoctor
dear doraemon, Thank you for the response. I...

dear doraemon,

Thank you for the response. I ended up with similar conclusion. It is a bit confusing for a non-bioinformatician like me.
Forum: Bioinformatics 12-23-2017, 05:13 AM
Replies: 2
Views: 1,216
Posted By krapulaxdoctor
Problem with UCSC GTF files?

Hi,

I would like to ask for some opinion and advice related to the different available GTF-file sources for annotated genes.(mm10, but others as well)
I did some search to avoid duplicate...
Forum: Bioinformatics 08-01-2017, 09:59 AM
Replies: 5
Views: 1,626
Posted By krapulaxdoctor
Hi, I hope to revive this thread, because I need...

Hi, I hope to revive this thread, because I need some advice:
I got a debate with colleagues about the very same question: which gene is expressed or not. When I mentioned that I used an FPKM cutoff...
Forum: Bioinformatics 01-22-2016, 01:07 AM
Replies: 6
Views: 2,058
Posted By krapulaxdoctor
Thank you for all the quick responses. It is a...

Thank you for all the quick responses.
It is a great help for me.

dariober:


Yes, that would be the main goal. Thanks.
Forum: Bioinformatics 01-21-2016, 02:56 AM
Replies: 6
Views: 2,058
Posted By krapulaxdoctor
Unhappy Samtools filter reads based on CIGAR values

Dear all,

I would like to ask for some help with samtools:

I found many threads about using samtools to filter reads based on some criteria, however, I did not find any clue how to filter reads...
Forum: Bioinformatics 10-23-2015, 05:03 AM
Replies: 0
Views: 649
Posted By krapulaxdoctor
picard metrics error

Dear all,
I would like to ask for help to solve this issue with Picard tools:

I already looked through forums, picard FAQ, but I id not find similar problems.

I would like to run the...
Forum: Bioinformatics 09-03-2015, 05:06 AM
Replies: 4
Views: 2,298
Posted By krapulaxdoctor
Thank you for the quick responses. I will look...

Thank you for the quick responses.
I will look after the mentioned programs.

Is there any software available that does count reads on introns the same way as it is mentioned in the case of...
Forum: Bioinformatics 09-03-2015, 01:26 AM
Replies: 4
Views: 2,298
Posted By krapulaxdoctor
count reads on exons and introns for each transcripts

Hi,

I would like to ask for an advice:

I have an RNA-seq bam-file and i have to count the exonic reads and intronic reads for each annotated refseq transcript.

So, in the end I would like to...
Forum: Bioinformatics 08-29-2015, 03:23 AM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
Hi, I am using: Version: 1.2 (using htslib...

Hi,

I am using:
Version: 1.2 (using htslib 1.2.1)
Forum: Bioinformatics 05-11-2015, 01:35 PM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
OK , I'll have a try. Thank you for all your help.

OK , I'll have a try. Thank you for all your help.
Forum: Bioinformatics 05-11-2015, 01:24 PM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
This is the last few lines...

This is the last few lines...
Forum: Bioinformatics 05-11-2015, 01:18 PM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
How do I do this " tail " ? Sorry im a...

How do I do this " tail " ?
Sorry im a beginner...
Forum: Bioinformatics 05-11-2015, 01:12 PM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
And also, when I try to convert these BAM files...

And also, when I try to convert these BAM files into BED files, it generates a file, but the program (bedtools bamtobed)gives this error message:

terminate called after throwing an instance of...
Forum: Bioinformatics 05-11-2015, 01:04 PM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
@SQ SN:chr1 LN:195471971 ...

@SQ SN:chr1 LN:195471971
@SQ SN:chr2 LN:182113224
@SQ SN:chr3 LN:160039680
@SQ SN:chr4 LN:156508116
@SQ SN:chr5 LN:151834684
@SQ SN:chr6 LN:149736546
@SQ SN:chr7 LN:145441459...
Forum: Bioinformatics 05-11-2015, 12:30 PM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
Actually, you were right. There must be a problem...

Actually, you were right. There must be a problem with the header. It can be converted to SAM but I cant convert it back to BAM. Also, I cant convert it into BED. Do you know any way to fix the...
Forum: Bioinformatics 05-09-2015, 05:12 AM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
Yes, samtools can convert them into SAM with...

Yes,
samtools can convert them into SAM with the:

BBmap can deal with these SAM files.
Forum: Bioinformatics 05-08-2015, 12:20 PM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
Yes, Brian, here it is: java -ea -Xmx200m...

Yes, Brian, here it is:

java -ea -Xmx200m -cp /home/user/Downloads/bbmap/current/ jgi.ReformatReads in=/home/user/Desktop/allbams/RNA.bam out=/home/user/Desktop/RNAout.bam minlength=1 maxlength=41...
Forum: Bioinformatics 05-08-2015, 11:25 AM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
Thank you for the response GenoMax. The code...

Thank you for the response GenoMax.
The code helped. However, I have samtools installed but the program gave an error message with my BAM files. Now i try to convert them to SAM to see if it works.
Forum: Bioinformatics 05-08-2015, 10:38 AM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
Hi, Thank you for the quick response. I...

Hi,

Thank you for the quick response.
I downloaded the BBMap tar from here: http://sourceforge.net/projects/bbmap/?source=typ_redirect

I used tar -xzf BBMap.tar.gz command.

Do I have to...
Forum: Bioinformatics 05-08-2015, 06:58 AM
Replies: 27
Views: 6,464
Posted By krapulaxdoctor
Filter BAM/SAM based on read length

Dear All,

I have a BAM file that contains reads with different length.
Could you please tell me how can I filter only those reads that are longer/shorter than a given value and write it in a new...
Showing results 1 to 20 of 20

 


All times are GMT -8. The time now is 02:23 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO