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Search: Posts Made By: Siva
Forum: Bioinformatics 03-13-2013, 09:44 AM
Replies: 13
Views: 3,081
Posted By Siva
Hi Chad... This will give a set of unique read...

Hi Chad...
This will give a set of unique read IDs but not always uniquely mapped (aligned reads). I think it depends (as you point out) on how we ask tophat to align.

In default mode tophat...
Forum: Bioinformatics 03-12-2013, 11:59 AM
Replies: 13
Views: 3,081
Posted By Siva
Thanks! I do understand your point about QC. ...

Thanks! I do understand your point about QC.

I have some tophat2 generated BAM files (50 base paired end RNA seq). I ran tophat with all default options. I want to get the number of uniquely...
Forum: Bioinformatics 03-11-2013, 02:32 PM
Replies: 13
Views: 3,081
Posted By Siva
Actually unmapped hits are written separately...

Actually unmapped hits are written separately under unmapped.bam. You can run samtools -flagstat on that and get the number of unmapped reads (QC pass + QC fail)
Forum: Bioinformatics 01-25-2013, 02:59 PM
Replies: 3
Views: 1,092
Posted By Siva
My immediate aim to find differentially expressed...

My immediate aim to find differentially expressed genes. However I am also interested in more depth. Will be useful in analyzing novel genes.

I will go through this paper. However, I was under the...
Forum: Bioinformatics 01-25-2013, 11:49 AM
Replies: 3
Views: 1,092
Posted By Siva
RNA seq: handling samples after re-sequencing

I set up an RNA seq experiment with 4 samples and 4 bioreplicates each. I now have a total of 16 fastq files. However, of these, 8 are going to be resequenced because number of reads were too low...
Forum: Bioinformatics 01-18-2013, 10:04 AM
Replies: 17
Views: 7,442
Posted By Siva
Hi Parthav I work on maize genome sequence...

Hi Parthav
I work on maize genome sequence available from http://ftp.maizesequence.org/current/assembly (http://ftp.maizesequence.org/current/assembly/). You will find the file...
Forum: Bioinformatics 01-17-2013, 02:25 PM
Replies: 17
Views: 7,442
Posted By Siva
Do keep us updated. Actually in my case the BAM...

Do keep us updated. Actually in my case the BAM file (appears to be correctly sorted) if you look at the headers. I did away with -G option for cufflinks (did not supply GFF file). I still get the...
Forum: Bioinformatics 01-15-2013, 01:04 PM
Replies: 17
Views: 7,442
Posted By Siva
Actually I thought I had the right idea....but I...

Actually I thought I had the right idea....but I just realized that the "sort order of reads in BAM" refers to the aligned reads vs the headers. The aligned reads and the headers in the BAM file must...
Forum: Bioinformatics 01-15-2013, 08:24 AM
Replies: 17
Views: 7,442
Posted By Siva
If you sort your GFF files in the same order as...

If you sort your GFF files in the same order as the BAM files you should be able to get it to work. Alternatively drop the GFF files.
Forum: Illumina/Solexa 01-13-2013, 03:45 PM
Replies: 4
Views: 1,740
Posted By Siva
Thanks! The reference fasta has the same number...

Thanks! The reference fasta has the same number of chromosomes as in the GFF. It was the ID issue that I failed to see though it was staring at me.
Forum: Illumina/Solexa 01-13-2013, 03:44 PM
Replies: 4
Views: 1,740
Posted By Siva
Smile Whew! Thanks I changed the ID ("1")in the GFF to...

Whew! Thanks I changed the ID ("1")in the GFF to the rather unwieldy string ("chromosome:AGPv2:1:1:301354135:1") as given in BAM and it worked!

Siva
Forum: Illumina/Solexa 01-13-2013, 07:01 AM
Replies: 4
Views: 1,740
Posted By Siva
Mismatch between BAM and GFF file

I am trying to use htseq-count to count the occurences of features (taken from my GFF file) in my BAM file:

I use the std htseq-count command viz;
samtools view file.bam | htseq-count [options] -...
Forum: Bioinformatics 01-12-2013, 03:47 PM
Replies: 191
Views: 73,129
Posted By Siva
Ok I got an answer from another thread; I have...

Ok I got an answer from another thread; I have now installed it successfully
Check this in case you are grappling with a similar problem
http://seqanswers.com/forums/showthread.php?t=23768
Forum: Bioinformatics 01-12-2013, 02:20 PM
Replies: 191
Views: 73,129
Posted By Siva
Clang errors when trying to build HTseq

Hi All
I have a mac (OSx10.8.2) and get the following error when trying to build HT seq (0.5.3p9). Looks like a gcc issue...Any suggestions please?
Forum: RNA Sequencing 12-07-2012, 09:17 AM
Replies: 4
Views: 4,827
Posted By Siva
Illumina V 1.8 and Solexa quality

In Illumina V 1.8 the reads quality scores are in Sanger Fastq format (off set of ASCII33 and not Phred 64) so using --solexa-quals instead of --solexa1.3-quals seems to work! I am still not sure if...
Forum: RNA Sequencing 12-06-2012, 10:08 AM
Replies: 4
Views: 4,827
Posted By Siva
Prep-read errors: Tophat

I have attached the first 20 lines of Illumina sequence reads (sample.txt), these are 100 base single end reads. These are from Illumina's new pipeline (Version 1.8). The sequences are in fastq...
Forum: Bioinformatics 10-15-2010, 08:38 PM
Replies: 0
Views: 4,236
Posted By Siva
Tophat options to report unaligned reads and controlling Bowtie options

I run Tophat from command line on our shared Linux environment queue. The gist is this:

$ ~/tophat -o ./tophat_out_s1 -p 4 --solexa1.3-quals ./genome_bwtind/<AGPv1_genome_ind> s_1_sequence.txt
...
Forum: Bioinformatics 08-18-2010, 10:58 AM
Replies: 2
Views: 2,617
Posted By Siva
BEDTools..coverageBed query

Hi
I have a question regarding the way BEDtools' coverageBed handles a short read that matches both gene A and Gene B. In such an instance could you let me know which of the following is true?

1....
Forum: Bioinformatics 05-24-2010, 12:53 AM
Replies: 12
Views: 6,111
Posted By Siva
Thanks John, I too don't know why the tag ID is...

Thanks John, I too don't know why the tag ID is missing.
Forum: Bioinformatics 05-24-2010, 12:47 AM
Replies: 12
Views: 6,111
Posted By Siva
As a followup: I work with maize which has 10...

As a followup: I work with maize which has 10 chromosomes. So when it says "11 sequences loaded" does it refer to chromosomes 1 through 10 and chr Unknown? There is a chunk of sequences in the maize...
Forum: Bioinformatics 05-24-2010, 12:12 AM
Replies: 12
Views: 6,111
Posted By Siva
Samtools....SAM to BAM...warning or error!! Can I ignore?

Hello All

I am trying to convert a Tophat SAM file to BAM and I get the warning message "The tag [ID] required for [PG] not present.". I have included it below. However then [sam_header_read2]...
Forum: Bioinformatics 05-11-2010, 11:55 PM
Replies: 1
Views: 2,272
Posted By Siva
RNA-seq ambiguous reads

Hi Aaron
I have done RNA-seq on maize endopserms. I would like to know how does coverageBed handle "ambiguous reads" in RNA-seq experiments? Is there a separate entry that lists such ambiguous...
Forum: Bioinformatics 05-08-2010, 02:44 PM
Replies: 12
Views: 4,201
Posted By Siva
Geng: You should try aligning your reads using...

Geng:
You should try aligning your reads using Tophat (since it also aligns reads spanning splice junctions). You should then use Cufflinks to assemble the Tophat SAM. If you only use bowtie or any...
Forum: Bioinformatics 05-06-2010, 02:33 PM
Replies: 20
Views: 15,605
Posted By Siva
Steven This works fine too. Thanks!! Will post...

Steven
This works fine too. Thanks!! Will post feedback soon.

Siva
Forum: Bioinformatics 05-06-2010, 02:31 PM
Replies: 20
Views: 15,605
Posted By Siva
[QUOTE=Simon Anders;18102]It seems that it's...

[QUOTE=Simon Anders;18102]It seems that it's still there. Try the following. Start a Python session and type:

import HTSeq
print HTSeq.__file__

This will print out where Python found HTSeq and...
Showing results 1 to 25 of 57

 


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