Forum: Bioinformatics
03-20-2018, 02:17 AM
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Replies: 37
Views: 32,003
Hi,
Can I use reformat or any other bbtools...
Hi,
Can I use reformat or any other bbtools script to split my fasta file into sub-files?
eg X.fa (100 sequences) -> X01.fa X02.fa....X10.fa (each with 10 sequences)?
I don't mind whether I...
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Forum: Bioinformatics
03-02-2018, 05:47 AM
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Replies: 5
Views: 2,934
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Forum: Bioinformatics
02-18-2018, 11:08 PM
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Replies: 5
Views: 2,934
Hi,
Thank you for the suggestion.
With...
Hi,
Thank you for the suggestion.
With the "-Xmx24052m threads=12" flag it runs with 12 threads and the memory but still has an ArrayIndexOutOfBoundsException in multiple threads...
:confused:...
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Forum: Bioinformatics
02-15-2018, 06:37 AM
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Replies: 5
Views: 2,934
BBDuk java error when filtering using entropy?
Hello,
I am having an issue with a java error when trying to use BBDuk to remove low entropy sequences from a fastq file. The libraries were made using ribozero so there are a number of polyT...
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Forum: Bioinformatics
02-14-2018, 02:28 AM
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Replies: 335
Views: 154,983
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Forum: Bioinformatics
07-04-2016, 10:54 PM
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Replies: 2
Views: 2,183
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Forum: Bioinformatics
07-04-2016, 07:12 AM
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Replies: 2
Views: 2,183
GC content of assembled transcripts
Hi,
I have a transcriptome assembly that is comprised of a metazoan and protist (intracellular symbiont) component. I know from the assemblies of similar organisms that the CG percentage of the...
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Forum: Bioinformatics
04-07-2016, 07:58 AM
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Replies: 2
Views: 2,104
Hi,
Well, I found (to my chagrin) that...
Hi,
Well, I found (to my chagrin) that cd-hit has an aux tools package containing the cd-hit-dup tool.
I do not, however, get the same results using cd-hit-est and cd-hit-dup.
If I use...
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Forum: Bioinformatics
04-07-2016, 06:58 AM
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Replies: 2
Views: 2,104
Dedupe on assembled RNA-Seq?
Hi,
I am trying to get rid of "redundant" sequences from a trinity assembly. I used dedupe.sh to get rid of duplicates in the illumina source files and got a very good result.
After assembling...
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Forum: Bioinformatics
10-02-2015, 05:39 AM
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Replies: 3
Views: 1,791
faSomeRecords = lifesaver
Thank you so much genomax - that took less than 2 seconds for each file. The other way was still chugging away after two days...
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Forum: Bioinformatics
10-02-2015, 04:33 AM
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Replies: 3
Views: 1,791
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Forum: Illumina/Solexa
09-06-2013, 02:44 AM
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Replies: 2
Views: 4,340
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