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Forum: Bioinformatics 09-29-2011, 09:47 AM
Replies: 5
Views: 4,211
Posted By macrowave
You didn't provide the reference sequences when...

You didn't provide the reference sequences when calling pileup? If that's the case, all the ref bases are Ns and you probably wouldn't get the right consensus.
Forum: Bioinformatics 09-29-2011, 09:34 AM
Replies: 10
Views: 3,067
Posted By macrowave
Maybe you can dig something out from the sam...

Maybe you can dig something out from the sam bitwise flags, I'm sure the strand information would be encoded there. For details, you can see the sam specifications here:...
Forum: Bioinformatics 09-28-2011, 09:19 AM
Replies: 10
Views: 3,067
Posted By macrowave
I think Bio::DB::Sam is the way to go, if you...

I think Bio::DB::Sam is the way to go, if you know a bit perl programming. You can use its methods to access sam/bam for any information, including map positions and strands.
Forum: Bioinformatics 08-29-2011, 05:04 AM
Replies: 3
Views: 6,382
Posted By macrowave
Looks like you don't have replicates. The...

Looks like you don't have replicates. The difference between raw counts and edgeR might be from the normalization you did in the edgeR process. So if no replicates, I wouldn't trust the results. For...
Forum: Bioinformatics 08-27-2011, 02:16 PM
Replies: 3
Views: 6,382
Posted By macrowave
You may filter the edge$table object within R...

You may filter the edge$table object within R using subset functions, I'm sure you'll get the right results. Usually, as a rule of thumb, I use P<=0.05 and logFC>=1 or logFC<=-1, in other words, fold...
Forum: Bioinformatics 08-27-2011, 02:14 PM
Replies: 6
Views: 4,841
Posted By macrowave
just run blastall you'll see all the options,...

just run blastall you'll see all the options, these are the old blast programs, now it's called blast+ suit, as mentioned above.
Forum: Bioinformatics 08-23-2011, 05:10 AM
Replies: 5
Views: 1,981
Posted By macrowave
and the sam flag 161 (1+32+128) means the paired...

and the sam flag 161 (1+32+128) means the paired reads mapped one forward, one reverse, but for some reason, the aligner thinks the pair isn't right (not properly aligned?), so that might be also a...
Forum: Bioinformatics 08-22-2011, 06:34 AM
Replies: 5
Views: 1,981
Posted By macrowave
Just realized that your problem might be a bug in...

Just realized that your problem might be a bug in TopHat. In the newest TopHat release notes, they say 'TLEN field in SAM format is correctly output', which means you may be using an older release...
Forum: Bioinformatics 08-22-2011, 04:56 AM
Replies: 5
Views: 1,981
Posted By macrowave
Can you provide more specific information, such...

Can you provide more specific information, such as the fragment size, read length, the expected insert sizes, reference type (genome or transcriptome)? Form my experience, paired-end mapping with...
Forum: Bioinformatics 08-19-2011, 07:14 AM
Replies: 1
Views: 2,599
Posted By macrowave
I had the similar idea when facing a somewhat...

I had the similar idea when facing a somewhat similar situation. In theory, this would work, but in practice, I found the transcript levels quantified from the 'reconstructed' genome are biased...
Forum: Bioinformatics 08-19-2011, 07:02 AM
Replies: 5
Views: 1,981
Posted By macrowave
Can you try using other short read mapper such as...

Can you try using other short read mapper such as bwa to see the insert size distribution? Or you can use the Bio::DB::Sam perl modules to access the entire sam/bam, and infer the insert size...
Forum: Bioinformatics 08-11-2010, 07:28 AM
Replies: 3
Views: 2,364
Posted By macrowave
You may not be able to do it as TopHat needs...

You may not be able to do it as TopHat needs Bowtie to run in a specific way. The only way to crack is to re-compile TopHat, changing the way it calls Bowtie, and you're at the risk of crashing...
Forum: Bioinformatics 06-10-2010, 09:18 AM
Replies: 1
Views: 3,357
Posted By macrowave
I think you need to bump up '--chunkmbs' value,...

I think you need to bump up '--chunkmbs' value, actually this was well explained in the manual.
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