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Forum: Illumina/Solexa 04-11-2016, 04:39 AM
Replies: 4
Views: 6,382
Posted By dschika
Ok, probably you want to use -v and -f, my bad. ...

Ok, probably you want to use -v and -f, my bad.

As you read the manual which you can find here (http://www.htslib.org/doc/samtools.html), you know what -v and -f do:
Forum: Illumina/Solexa 04-11-2016, 12:56 AM
Replies: 4
Views: 6,382
Posted By dschika
Check samtools mpileup man page. You may want...

Check samtools mpileup man page.
You may want to try -f instead of -v ?
Forum: Introductions 10-20-2015, 12:48 AM
Replies: 4
Views: 1,297
Posted By dschika
root/reference/dbname vs. ...

root/reference/dbname vs. /root/reference/db/dbname

May that be your problem?

What happens if you just type:

-db dbname
Forum: Bioinformatics 10-19-2015, 07:28 AM
Replies: 7
Views: 1,274
Posted By dschika
Also quite nice!

Also quite nice!
Forum: Bioinformatics 10-19-2015, 07:01 AM
Replies: 7
Views: 1,274
Posted By dschika
Is GenoMax's assumption right? That may cause...

Is GenoMax's assumption right? That may cause problems...

Just in case:
sed 's/^\([ATGC]*\)N\([ATGCN]*\)/\1/g' test.fa
>R1
GGGGGGGTTTTTTTTTTTTTTT
>R2
GGGGGGGGGGTTTTTTTTTT
Forum: Bioinformatics 10-18-2015, 10:50 PM
Replies: 7
Views: 1,274
Posted By dschika
You could try: sed...

You could try:

sed 's/^\([ATGC]*\)N\([ATGCN]*\)/\1/g' YOURFILE > NEWFILE

at least if you have a *nix operating system.
Forum: Bioinformatics 06-13-2015, 12:51 AM
Replies: 10
Views: 4,057
Posted By dschika
I understood that it produces output. But I would...

I understood that it produces output. But I would like to know if you have any hits at all. If you don't have hits, you won't get any output in the second case.

How often can you find the phrase...
Forum: Bioinformatics 06-12-2015, 01:10 AM
Replies: 10
Views: 4,057
Posted By dschika
Were there any hits reported in the output of the...

Were there any hits reported in the output of the first command? If there were no hits at all, I guess the tabular output format will not produce a file.
Forum: Bioinformatics 06-09-2015, 09:37 AM
Replies: 6
Views: 1,390
Posted By dschika
Indeed, if you are interested in only a handful...

Indeed, if you are interested in only a handful of loci that sounds reasonable. Thanks for clarification.
Forum: Bioinformatics 06-09-2015, 12:41 AM
Replies: 6
Views: 1,390
Posted By dschika
Even though I don't know how large your sample...

Even though I don't know how large your sample is, 5 days for demultiplexing sounds very long, even for very large data sets. Maybe you could speed up the script?

Two questions just for curiosity:...
Forum: 454 Pyrosequencing 06-05-2015, 12:53 AM
Replies: 13
Views: 12,808
Posted By dschika
Maybe this thread helps? ...

Maybe this thread helps?
http://seqanswers.com/forums/showthread.php?t=25339
Forum: Bioinformatics 06-05-2015, 12:09 AM
Replies: 5
Views: 1,325
Posted By dschika
Have you tried piping bwa mem output into...

Have you tried piping bwa mem output into samtools? Something like:

bwa mem [your options] | samtools view -SF 4 - > output.sam
Forum: 454 Pyrosequencing 06-05-2015, 12:00 AM
Replies: 3
Views: 5,397
Posted By dschika
give it a try with ubuntu. ah, you already did: ...

give it a try with ubuntu. ah, you already did:

http://seqanswers.com/forums/showthread.php?t=32727
Forum: 454 Pyrosequencing 06-04-2015, 11:18 PM
Replies: 3
Views: 5,397
Posted By dschika
You can request a free version on their website:...

You can request a free version on their website: http://www.454.com/products/analysis-software/
Forum: Bioinformatics 06-04-2015, 11:12 PM
Replies: 5
Views: 1,325
Posted By dschika
Have a look at: ...

Have a look at:
https://www.biostars.org/p/56246/
Forum: Bioinformatics 06-04-2015, 12:34 AM
Replies: 3
Views: 1,047
Posted By dschika
Assuming your vcf files contain only the filtered...

Assuming your vcf files contain only the filtered SNPs of a single strain you are interested in, you could try:


# Get number of different (!) SNPs of two vcfs
cat 1.vcf 2.vcf | grep -v '^#' |...
Forum: General 03-15-2015, 08:20 AM
Replies: 6
Views: 1,605
Posted By dschika
Correct, you're welcome!

Correct, you're welcome!
Forum: General 03-15-2015, 08:02 AM
Replies: 6
Views: 1,605
Posted By dschika
No problem, I just realized, that I was thinking...

No problem, I just realized, that I was thinking way to complicated:

sed 's/\.1 / /g' YOURINPUT.fastq > out.fastq

Just replace ".1 " with " " and escape the "." with a backslash.
Forum: General 03-15-2015, 06:11 AM
Replies: 6
Views: 1,605
Posted By dschika
This command should do the job: awk '{if ($1...

This command should do the job:

awk '{if ($1 ~ /SRR/) {split($0, T, ".1 "); print T[1], T[2]} else print $0}' YOURINPUT.fastq

Since you mentioned sed and awk I assume you know that $1 = first...
Forum: Bioinformatics 03-13-2015, 09:11 AM
Replies: 7
Views: 4,586
Posted By dschika
You could try CD-HIT to cluster the reads.

You could try CD-HIT to cluster the reads.
Forum: Bioinformatics 03-13-2015, 06:43 AM
Replies: 2
Views: 1,021
Posted By dschika
Thanks for your comment, GenoMax. I also think...

Thanks for your comment, GenoMax. I also think that reviewers would not be too happy with anyone changing raw data. And I also do not like the idea so much.

Unfortunately, re-running is not a...
Forum: Bioinformatics 03-13-2015, 05:28 AM
Replies: 2
Views: 1,021
Posted By dschika
Replace N's in R2 read, if I know the sequence

Hi,

I have a library which was constructed using a restriction enzyme (ApeKI). A paired-end 100 bp Illumina sequencing was performed.
The R1 (first read of a pair) reads consisted of a barcode...
Forum: Bioinformatics 11-25-2014, 01:12 AM
Replies: 7
Views: 2,870
Posted By dschika
Are the names of the samples in the vcf and the...

Are the names of the samples in the vcf and the population files exactly the same?
Forum: Bioinformatics 09-23-2014, 12:40 AM
Replies: 7
Views: 2,870
Posted By dschika
If the numbers in the vcf file are already...

If the numbers in the vcf file are already different, you do not have issues with VCFtools.

Do you apply any filters during vcf file generation, e.g. minimum coverage per individual?
Forum: Bioinformatics 09-22-2014, 03:29 AM
Replies: 7
Views: 2,870
Posted By dschika
I also think [VCFtools] mailing list is best for...

I also think [VCFtools] mailing list is best for questions about VCFtools.

Nevertheless, how were the vcf files generated? Did you merge your single individual vcf files into one containing all 8...
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