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Search: Posts Made By: k_a_r_o_l
Forum: Bioinformatics 12-20-2018, 11:55 PM
Replies: 0
Views: 680
Posted By k_a_r_o_l
STAMP installation Fedora 27

Hello,

Does anyone know how to install STAMP on fedora 27? I tried:
dnf install libblas-dev liblapack-dev gfortran
dnf install freetype* python-pip python-dev python-numpy python-scipy...
Forum: Bioinformatics 05-22-2018, 07:07 AM
Replies: 0
Views: 477
Posted By k_a_r_o_l
Qiime - works only on root

Hi,

My Qiime works only on root. How to change it to have ana access as localhost?

best
Forum: Bioinformatics 05-22-2018, 12:44 AM
Replies: 0
Views: 439
Posted By k_a_r_o_l
Eliminate contigs having certain level of identity from the dataset

Hi,

Does anybody know how to eliminate from the dataset of contigs those having the 90% identity and being shorter than the "reference" contig?

best
Forum: Bioinformatics 05-16-2018, 03:38 AM
Replies: 1
Views: 620
Posted By k_a_r_o_l
OK. I've found a solution. In a script...

OK. I've found a solution. In a script accession2.taxid.make change the line:

SORT := grep -v accession | sed 's/\.[[:digit:]]*//' | LC_ALL=C sort
to
SORT := grep -v accession | sed...
Forum: Bioinformatics 05-15-2018, 06:22 AM
Replies: 1
Views: 620
Posted By k_a_r_o_l
Krona updateAccessions.sh

Hello,

I am trying to do updateAccessions.sh in Krona. Unfortunately during that process (sorting) I don't have enough space in /tmp so everything stops.

Do you have any tips how to run this...
Forum: Bioinformatics 02-07-2018, 10:08 PM
Replies: 4
Views: 940
Posted By k_a_r_o_l
Thx. for help Finally I used SGA preprocess...

Thx. for help

Finally I used SGA preprocess with --dust option and I think it helped.
Forum: Bioinformatics 02-07-2018, 03:59 AM
Replies: 4
Views: 940
Posted By k_a_r_o_l
fastq files

fastq files
Forum: Bioinformatics 02-07-2018, 03:54 AM
Replies: 4
Views: 940
Posted By k_a_r_o_l
Removing reads with repeats

Hello,

Can anyone help me. In my data I have reads like:

CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACCCAC

ACACACACACACACACAC
...
Forum: Bioinformatics 04-20-2017, 04:54 AM
Replies: 0
Views: 950
Posted By k_a_r_o_l
Problem while loading BIOM file in STAMP

Hello,

When I am loading my BIOM file in STAMP everything goes well and I am able to generate .spf file but when I want to open this file I get an error message:

"Field to correctly parse...
Forum: Bioinformatics 04-14-2017, 12:15 AM
Replies: 0
Views: 934
Posted By k_a_r_o_l
Qiime - plot_taxa_summary.py problem

Hello everyone!

I am trying to analyze my samples using Qiime prtocol for 16S metagenomic data. I have problem with plot_taxa_summary.py command. I try to analyze only 1 sample - approx. 150.000...
Forum: Metagenomics 04-11-2017, 08:37 AM
Replies: 3
Views: 1,830
Posted By k_a_r_o_l
primes that target 16S V3 and V4 region (used in...

primes that target 16S V3 and V4 region (used in illumina 16S metagenomic protocol)
Forum: Metagenomics 04-11-2017, 06:39 AM
Replies: 3
Views: 1,830
Posted By k_a_r_o_l
Read lenght in 16S RNA data

Hi,

My amplicon after assembly shoud have approx. 460bp. Do I have to analyze only 460bp products or can I also analyze some shorter/longer amplicons. If yes, how to set a specific lenght...
Forum: Bioinformatics 03-10-2015, 10:31 PM
Replies: 3
Views: 996
Posted By k_a_r_o_l
I am sure that second barcode is unique. Thank...

I am sure that second barcode is unique. Thank You, I will try this.
Forum: Bioinformatics 03-10-2015, 09:19 AM
Replies: 3
Views: 996
Posted By k_a_r_o_l
Only one barcode present after dual indexing

Hi,

I have such a problem. I had my MiSeq experiment where I was sequencing some amplicons which were dual indexed (each sample had 2 unique barcodes)

Something like this:
sample1 - AB...
Forum: Bioinformatics 03-02-2015, 04:46 AM
Replies: 4
Views: 1,181
Posted By k_a_r_o_l
My library has a lot of short inserts, and this...

My library has a lot of short inserts, and this is why some of my reads have nextera transposase sequence in it. Depending on insert I observe different lengths of nextera sequences in my reads so it...
Forum: Bioinformatics 03-02-2015, 04:14 AM
Replies: 4
Views: 1,181
Posted By k_a_r_o_l
How to remove some sequences

Hello,

Maybe someone can help me. Do You know any software, method how to remove from FASTQ files reads with certain motif. I dont want to trimm my reads but rather remove whole sequences with...
Forum: Bioinformatics 04-30-2014, 04:43 AM
Replies: 0
Views: 1,388
Posted By k_a_r_o_l
Interpretation of FASTQC - Overrepresented Kmers

Hello Everyone,

I am very new at NGS data procesing and I have a problem with my quality results.

Short summary about my experiment:
My starting material is a low quantity of RNA. In first...
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