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Forum: Bioinformatics 11-13-2018, 06:19 AM
Replies: 330
Views: 111,218
Posted By dariober
bbduk with bzip2 input file

Hi- Is bzip2 input supported by `bbduk.sh`? When I try it, bbduk seems to hang as below. (It would be good to have support for bzip2)

Thanks!

bbduk.sh...
Forum: Bioinformatics 10-16-2017, 12:28 AM
Replies: 330
Views: 111,218
Posted By dariober
Hi Genomax- These are R1 and R2 real identifiers:...

Hi Genomax- These are R1 and R2 real identifiers:

@E00295:75:H7LLTALXX:8:1101:4553:1643 1:N:0:8
@E00295:75:H7LLTALXX:8:1101:4553:1643 2:N:0:8

I think one issue is that the interleaved format...
Forum: Bioinformatics 10-15-2017, 06:30 AM
Replies: 330
Views: 111,218
Posted By dariober
Different output with interleaved input

Hello again-

I think there is an inconsistent behavior in how bbduk handles interleaved input depending on whether the interleaved option is set to "true" or "auto".

Consider the case where...
Forum: Bioinformatics 10-05-2017, 10:37 PM
Replies: 674
Views: 170,084
Posted By dariober
Hi Brain- Thanks for the comments (and for the...

Hi Brain- Thanks for the comments (and for the tools of course!). I see your point but I still think the current default behaviour of bbmap is incorrect when sequence names have spaces because it...
Forum: Bioinformatics 10-05-2017, 03:48 AM
Replies: 674
Views: 170,084
Posted By dariober
Sorry... another issue. I have a reference...

Sorry... another issue.

I have a reference genome where the header lines contain spaces, like this:

>chr1 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome ...
Forum: Bioinformatics 10-05-2017, 03:40 AM
Replies: 674
Views: 170,084
Posted By dariober
Hi Brain, thanks for feedback. I thought it was...

Hi Brain, thanks for feedback. I thought it was harmless the problem is that I have a pipeline (snakemake) that will "refuse" to proceed on receiving this error.
Forum: Bioinformatics 10-03-2017, 07:20 AM
Replies: 674
Views: 170,084
Posted By dariober
bbduk.sh: "reads" parameter does not exit clean

Hi- Not sure this thread is the best place to post this...

It seems to me that the `reads` parameter makes bbduk exits with an error when the input is not fully processed.

These runs are both...
Forum: Academic/Non-Profit Jobs 10-21-2016, 03:03 AM
Replies: 0
Views: 607
Posted By dariober
Computational Biologist - Cambridge University/CRUK

Research Associate - Computational Biologist (Fixed Term)


We seek a highly motivated computational researcher for a key role within Professor Balasubramanian's pioneering research programme at...
Forum: Bioinformatics 08-08-2016, 02:39 AM
Replies: 6
Views: 2,153
Posted By dariober
My 2p: EndNote: Myself and others around me...

My 2p:

EndNote: Myself and others around me have switched to Mendeley (https://www.mendeley.com/) and we are quite happy with it. I haven't been too impressed by Endnote and sometimes I got...
Forum: Bioinformatics 07-19-2016, 11:30 PM
Replies: 2
Views: 1,736
Posted By dariober
In addition to Devon's insightful answer, I would...

In addition to Devon's insightful answer, I would add a couple of possible reasons:

* limma, edger and DESeq have been used very extensively and they have very good reputation (well deserved)....
Forum: Bioinformatics 06-12-2016, 11:23 PM
Replies: 1
Views: 1,355
Posted By dariober
See this thread...

See this thread http://seqanswers.com/forums/showthread.php?t=59219

I don't know of any tool box readily available though.
Forum: Bioinformatics 06-12-2016, 11:15 PM
Replies: 5
Views: 1,948
Posted By dariober
Hi- Is that a problem? The OP asks for the number...

Hi- Is that a problem? The OP asks for the number of reads containing pattern. So if a read contains the pattern twice it should still be counted as 1, which is what grep -c does, isn't it?
Forum: Bioinformatics 03-29-2016, 06:27 AM
Replies: 3
Views: 1,200
Posted By dariober
You don't need to change the source code...

You don't need to change the source code yourself, rather you download the repository version, install it and run this on the server. This procedure might be something on these lines:

* Download
...
Forum: Bioinformatics 03-29-2016, 04:57 AM
Replies: 3
Views: 1,200
Posted By dariober
On macs2 callapeak try to set the temporary...

On macs2 callapeak try to set the temporary directory via the --tempdir option. Currently --tmpdir option is available in the code from the source repository on github...
Forum: Bioinformatics 03-11-2016, 04:36 AM
Replies: 8
Views: 2,266
Posted By dariober
As a side comment, you can make bwa mem more...

As a side comment, you can make bwa mem more sensitive by lowering the minimum score for a read to be outputted (-T option, e.g. try -T 20) and/or by making the seed length shorter (-k option). It...
Forum: Bioinformatics 03-03-2016, 11:22 PM
Replies: 1
Views: 724
Posted By dariober
In general I would say yes, if possible. Since...

In general I would say yes, if possible. Since you want to detect differences between states you should keep everything the same between cells except for the "state" variable I.e. randomize possible...
Forum: Bioinformatics 03-02-2016, 03:05 AM
Replies: 4
Views: 5,252
Posted By dariober
Just to expand a bit on Devon's answer......

Just to expand a bit on Devon's answer... Alignment score is a metric that tells you how similar the read is to the reference. AS increases with the number of matches and decreases with the number of...
Forum: Genomic Resequencing 03-02-2016, 12:02 AM
Replies: 1
Views: 3,492
Posted By dariober
The mapping quality is 0 meaning that there are...

The mapping quality is 0 meaning that there are multiple and equally probable alignments. In this case bwa picks one location at random and this could explain why different reads with the same...
Forum: Bioinformatics 02-25-2016, 02:49 AM
Replies: 1
Views: 764
Posted By dariober
You could use: newHeader=...

You could use:


newHeader= dnaHeader[0:locate] + '-aa' + dnaHeader[locate:]


Maybe it's not the most efficient strategy since you need to create a new string but unless your file is massive...
Forum: General 02-23-2016, 06:38 AM
Replies: 10
Views: 13,091
Posted By dariober
Just as a comment, if I'm not mistaken your...

Just as a comment, if I'm not mistaken your scripts reverse-complements the regular expression, which is something that cannot be done. I'd rather reverse complement the reference sequence even if it...
Forum: Bioinformatics 01-21-2016, 07:56 AM
Replies: 6
Views: 2,822
Posted By dariober
True, but I surmise the OP wants to select reads...

True, but I surmise the OP wants to select reads spanning different exons as opposed those only assigned to one exon. If this is the case, I think tophat uses N to mark gaps between exons (don't know...
Forum: Bioinformatics 01-21-2016, 06:24 AM
Replies: 6
Views: 2,822
Posted By dariober
Gapped reads are those containing the N operator...

Gapped reads are those containing the N operator in the cigar string right? You could do this:


samtools view -h in.bam \
| awk '{if($0 ~ /^@/ || $6 ~ /N/) {print $0}}' \
| samtools view -Sb -...
Forum: General 01-20-2016, 12:49 AM
Replies: 1
Views: 1,892
Posted By dariober
You can get chromosome sizes from UCSC with...

You can get chromosome sizes from UCSC with something like this (credit: bedtools docs):


mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
"select chrom, size from mm9.chromInfo" >...
Forum: Metagenomics 01-14-2016, 04:17 AM
Replies: 2
Views: 1,667
Posted By dariober
By gut feeling I would favour option 2 (more mice...

By gut feeling I would favour option 2 (more mice but fewer time points, right?) but obviously it depends on how much variation you expect between mice and between time points. If mice are very very...
Forum: General 11-20-2015, 05:28 AM
Replies: 1
Views: 968
Posted By dariober
This has been asked before in different flavours....

This has been asked before in different flavours. If you are ok using shell/bash, try this:


awk -v RS=">" 'NR>1 {sub("\n", "\t"); gsub("\n", ""); print ">"$0}' test.fa \
| awk -v FS="\t" '$2 ~...
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