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Forum: Bioinformatics 12-04-2019, 12:06 PM
Replies: 2
Views: 944
Posted By sdmoore
Recover only longest version of sequence from multiple sequence fasta file - help

Greetings,
I have a large list of fasta sequences (not paired end) from which I want to isolate the longest version of each "sequence" (obviously the longest one has a different sequence). For...
Forum: Bioinformatics 07-14-2014, 05:27 AM
Replies: 3
Views: 960
Posted By sdmoore
the PRICE was right

I wanted to update the thread to say that PRICE did the trick.

At first, I had trouble getting contains to extend into certain regions (which were ambiguous in the maps as well). After...
Forum: Bioinformatics 07-09-2014, 07:52 AM
Replies: 3
Views: 960
Posted By sdmoore
Thanks kopi-o. The description seems right,...

Thanks kopi-o.
The description seems right, thanks! It won't compile here at work (and not in mood to deal with yet another install project), so I'll check it out when I get home.

S
Forum: Bioinformatics 07-08-2014, 02:31 PM
Replies: 3
Views: 960
Posted By sdmoore
Possible to force contig builds from a selected region?

Hello SEQers,

We have a series of 10 bacterial genomes sequenced with Illumina (300-base PE reads, before read processing). We want to find SND/InDels responsible for a phenotype in 7 of them.
...
Forum: Bioinformatics 07-07-2014, 05:53 AM
Replies: 24
Views: 12,339
Posted By sdmoore
Thanks Brian and dpryan. I had to give up on...

Thanks Brian and dpryan.
I had to give up on bbmap for now, not for this problem (I found the AddOrReplaceReadGroups tool later: I edited the sams or the bams). Rather, the resulting vcf from...
Forum: Bioinformatics 07-07-2014, 05:39 AM
Replies: 9
Views: 5,120
Posted By sdmoore
BBduk goose.

Thanks Brian,

That's much clearer and makes sense.

I noticed that fastqc complained more about kmers after the normalization, and I can see why that could happen.
Forum: Bioinformatics 07-05-2014, 10:35 AM
Replies: 9
Views: 5,120
Posted By sdmoore
BBnorm target depth setting

Hi Thread/Brian,

I ran BBnorm on a pre-BBduk'd pair of reads. I plan to use the normalized reads for assemblers (Velvet or A5, well, A4 in this case).

./bbnorm.sh in1=R1_bbduk20.fq...
Forum: Bioinformatics 07-05-2014, 09:25 AM
Replies: 24
Views: 12,339
Posted By sdmoore
Possible to add Read Group in BBmap header?

*sorry, probably wrong thread, I found more activity in the release announcement thread*

Hello,
I used BBduk to process my read pairs and then mapped them using BBmap, then sam/bam and sorted.
I...
Forum: Bioinformatics 06-16-2014, 07:41 AM
Replies: 0
Views: 742
Posted By sdmoore
re-clipping the same library removes even more?

I am working with Illumina libraries on Galaxy.org.

I have used clip to remove Illumina adapters from the data set, it removed "too shorts, adapter-only, and the N-reads", (it removed >90,000). ...
Forum: Bioinformatics 06-16-2014, 07:32 AM
Replies: 2
Views: 975
Posted By sdmoore
Thanks for that paper, I had it in my folder, so...

Thanks for that paper, I had it in my folder, so I must have at least skimmed it.
I have not gotten decent assemblies using the paired end libraries (processed), I think they may all have to be the...
Forum: Bioinformatics 06-16-2014, 06:26 AM
Replies: 2
Views: 975
Posted By sdmoore
Won't assembling reads to a reference remove SNPs and InDels?

When aligning reads to a reference to generate a config for SNP/InDel detection, won't the alignment necessarily remove the reads that have the desired information?

I see this as a commonly-listed...
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