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Forum: Bioinformatics 01-16-2018, 02:58 PM
Replies: 636
Views: 126,103
Posted By mcmc
yes I know the scores may be different... but I'm...

yes I know the scores may be different... but I'm simply wondering whether the idfilter and subfilter post-filtering options work on the soft-clipped alignments or the non-clipped alignments. I want...
Forum: Bioinformatics 01-11-2018, 12:48 PM
Replies: 636
Views: 126,103
Posted By mcmc
bbmap local + idfilter

Brian et al., I am using the 'local' option with bbmap because I sometimes have a couple bases of adapter remaining (after bbduk mink=6) and my understanding is that 'local' will trim the ends to...
Forum: Bioinformatics 12-18-2017, 10:01 AM
Replies: 2
Views: 1,618
Posted By mcmc
Is there a way to modify the clearzone,...

Is there a way to modify the clearzone, specifically to force a map to the higher scoring alignment? I am trying to use bbsplit & bbmap with several closely related (cultured) strains and I would...
Forum: Bioinformatics 12-13-2017, 12:36 PM
Replies: 212
Views: 53,844
Posted By mcmc
Thanks! I'm surprised there's something BBTools...

Thanks! I'm surprised there's something BBTools doesn't do :)
Forum: Bioinformatics 12-13-2017, 08:29 AM
Replies: 212
Views: 53,844
Posted By mcmc
summarizing mapped reads by orf

Is there a way to use BBtools to summarize reads mapped to a genome (using BBmap/BBsplit, in a sam file) by orf? I see that pileup.sh will take a prodigal-output fasta file with orf info, but I've...
Forum: Bioinformatics 12-11-2017, 08:21 PM
Replies: 212
Views: 53,844
Posted By mcmc
BBSplit ambig=toss

Hi Brian et al.,
When I run BBsplit with ambig=toss, the ambiguous reads are not written to unmapped.fq; but when I run BBmap, they are. Is this the expected behavior? I'd like to be able to...
Forum: Bioinformatics 11-20-2017, 09:38 AM
Replies: 301
Views: 77,960
Posted By mcmc
Seal not printing outu file

Hi - I'm running seal to map reads to ref genomes. this is the command I ran:

seal in="${samplename}_nonribo.fq.gz" ref="${all4genomes}" pattern="${samplename}_out_%.fq.gz"...
Forum: Bioinformatics 02-11-2017, 03:58 PM
Replies: 16
Views: 4,382
Posted By mcmc
Thanks. This was HiSeq 2500 2x250 RapidRun (with...

Thanks. This was HiSeq 2500 2x250 RapidRun (with both lanes concatenated, which I assume is ok, since you refer to "flowcell" and not "lane"). I used the entire dataset (15 metagenomes) to calc the...
Forum: Bioinformatics 02-11-2017, 02:52 PM
Replies: 16
Views: 4,382
Posted By mcmc
Hello Brian, I get the message "Warning: Zero...

Hello Brian,
I get the message "Warning: Zero reads processed." using indump=dump.flowcell. But it looks like making the dump file worked ok (it says it processed 780m reads). Is it safe to ignore...
Forum: Bioinformatics 02-05-2017, 11:16 AM
Replies: 94
Views: 19,518
Posted By mcmc
Thanks. The data are from a metagenome with no...

Thanks. The data are from a metagenome with no good reference, so mapping to get error rates is not an option. My impression was that most(?) 2x250 HiSeq suffered from problems on the reverse read...
Forum: Bioinformatics 02-04-2017, 11:15 PM
Replies: 94
Views: 19,518
Posted By mcmc
Indeed, reducing it to -Xmx50g solved the problem...

Indeed, reducing it to -Xmx50g solved the problem (on a 64g exclusive node).

I've tried to improve my merging rate above ~75% and as you suspected I think poor quality is limiting the merging....
Forum: Bioinformatics 02-02-2017, 09:57 AM
Replies: 94
Views: 19,518
Posted By mcmc
I tried the command you suggested, and after...

I tried the command you suggested, and after first running out of memory (with -Xmx54g) and retrying with prealloc=t, now I get this error:

Initial size set to 19219231
Initial:
Ways=71,...
Forum: Bioinformatics 02-01-2017, 10:45 AM
Replies: 94
Views: 19,518
Posted By mcmc
Hi Brian, I have a very basic question about...

Hi Brian,
I have a very basic question about how merging works with the tadpole extend option. I have 2x250 HiSeq metagenome data, and about 75-80% of the reads merge by overlap after adapter...
Forum: Bioinformatics 01-30-2017, 09:35 AM
Replies: 16
Views: 4,382
Posted By mcmc
Brian et al., would you recommend filterbytile.sh...

Brian et al., would you recommend filterbytile.sh be done first, before adapter trimming & quality filtering?
Thanks,
MC
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