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Search: Posts Made By: thedamian
Forum: Bioinformatics 08-03-2016, 06:57 AM
Replies: 1
Views: 1,332
Posted By thedamian
samtools depth -Q 0 and -Q 1 output discrepancy

Hi
I have an exons_merged.bed file of total regions length 81036853:
awk 'BEGIN{sum=0}{sum+=$3-$2}END{print sum}' exons_merged.bed
81036853

Based on this merged BED file I do:
samtools depth...
Forum: Bioinformatics 06-27-2016, 07:59 AM
Replies: 0
Views: 886
Posted By thedamian
(SnpEff) SnpSift annotates only the first .vcf line

Hi,
I want to annotate my .vcf file based on ExAC database.
I'm ONLY interested in AC_EAS tags from the database

I do:
java -jar SnpSift.jar annotate -info AC_EAS ExAC_db.vcf.gz my.vcf.gz...
Forum: Bioinformatics 05-12-2015, 09:53 AM
Replies: 15
Views: 21,662
Posted By thedamian
Well, it was my guessing, don't know if will...

Well, it was my guessing, don't know if will work;)
anyway, try also:
a) try to use older version of picard
b) try to add picard's folder with .jar files to your env path
c) or use full path to...
Forum: Bioinformatics 05-12-2015, 02:09 AM
Replies: 15
Views: 21,662
Posted By thedamian
I believe here:...

I believe here: http://sourceforge.net/projects/picard/files/picard-tools/
Forum: Bioinformatics 05-12-2015, 01:41 AM
Replies: 15
Views: 21,662
Posted By thedamian
maybe try do download older versions and copy...

maybe try do download older versions and copy SortSam.jar to a new version folder. And maybe then try to execute it from the picard folder - It is just my first guess, don't know if will help ;)
Forum: Bioinformatics 10-16-2014, 02:42 AM
Replies: 1
Views: 1,487
Posted By thedamian
Hi I have the same question, is there a tool to...

Hi I have the same question, is there a tool to filter only the longest isoforms from a protein set?
Forum: Bioinformatics 04-07-2014, 01:26 AM
Replies: 4
Views: 2,403
Posted By thedamian
mapped reads statistics (from .bam)

Hi,

Do you know if it is possible to obtain such statistics from the .bam file:

Total Unique - total reads aligning to only a single location in the reference
U0 - # of unique hits with 0...
Forum: Bioinformatics 02-21-2014, 06:58 AM
Replies: 0
Views: 707
Posted By thedamian
RNA structural alignment

Hi,
Can you recommend me a program for RNA structural alignment?

For example:
I have a known RNA structure (from PDB or soft) with its coordinates in .ct, .bp etc, and I want to align to this...
Forum: Bioinformatics 01-21-2014, 04:57 AM
Replies: 3
Views: 2,474
Posted By thedamian
wc -l picard_un1.fastq 15367376...

wc -l picard_un1.fastq
15367376 picard_un1.fastq

wc -l bedtools_un1.fastq
11515208 bedtools_un1.fastq

headers are the same :)
Forum: Bioinformatics 01-21-2014, 03:11 AM
Replies: 3
Views: 2,474
Posted By thedamian
Difference between "bedtools bamtofastq" and Picard's SamToFastq

Hi,
I need to assembly some unmapped reads from Tophat2's output "unmapped.bam"
Firstly I have to extract read pairs from unmapped.bam

I found two tools for it:
bedtools bamtofastq -i...
Forum: Bioinformatics 12-18-2013, 01:51 AM
Replies: 1
Views: 1,037
Posted By thedamian
tophat2 reads count

Hi all,

I have two .fastq files of Illumina pair-end data (reads1.fastq & reads1.fastq).
All files together have 28803268 reads.

The output of Tophat2 are accepted_hits.bam and unmappted.bam....
Forum: Bioinformatics 11-12-2013, 04:01 AM
Replies: 1
Views: 1,075
Posted By thedamian
RNA secondary structure formats

Hello all,

I have following names of RNA molecules: HOTAIR, TETp4p6, TETp9_9, SRA, B2, U1.
Where I can find their structure formats? (.dp, .ct or .bp).
Where I can find synonyms of their name?
...
Forum: Bioinformatics 10-09-2013, 01:06 AM
Replies: 18
Views: 15,499
Posted By thedamian
@vd4mindia: I don't know, maybe try to index it....

@vd4mindia: I don't know, maybe try to index it. You shoud have in your directory files SRR062634_marked.sorted.bam and SRR062634_marked.sorted.bai.
If this won't help I'm not able to solve this...
Forum: Bioinformatics 10-07-2013, 01:49 PM
Replies: 18
Views: 15,499
Posted By thedamian
set these paramaters:...

set these paramaters: http://pokazywarka.pl/1ve6r7/ and then click "get output". Adjust your parameters and then click "get BED".
Forum: Bioinformatics 09-13-2013, 01:27 AM
Replies: 13
Views: 16,550
Posted By thedamian
Hi All, I have the same problem with BWA mem. I...

Hi All,
I have the same problem with BWA mem. I used -M option but still I get: .PicardException: Value was put into PairInfoMap more than once. 1: null:M00840:39:000000000-A5TE9:1:2103:11538:25521...
Forum: Bioinformatics 05-23-2013, 12:54 AM
Replies: 4
Views: 2,090
Posted By thedamian
I want olny five genes, so this simple approach...

I want olny five genes, so this simple approach seems to be fine. I'll check it:)
Forum: Bioinformatics 05-22-2013, 12:41 AM
Replies: 4
Views: 2,090
Posted By thedamian
I have 27050 contigs that have length of 1000 or...

I have 27050 contigs that have length of 1000 or more bases. The longest is 90691. So lenghts are good. They were generated by De Novo assembler embedded in CLC Genomic Workbench (reads are from...
Forum: Bioinformatics 05-21-2013, 06:01 AM
Replies: 4
Views: 2,090
Posted By thedamian
Find genes in contigs based on homology proteins

Hello,
I have contigs from a new organism (its genome isn't known well).
I know, that this organism produces some proteins that are similar to proteins of other organisms.

I would like to find...
Forum: Bioinformatics 04-10-2013, 12:44 AM
Replies: 2
Views: 1,423
Posted By thedamian
Seems promising. I will examine Web Serivices...

Seems promising. I will examine Web Serivices they provide.
Thank you
Forum: Bioinformatics 04-09-2013, 06:05 AM
Replies: 2
Views: 1,423
Posted By thedamian
HGVS to hg19 conversion

Hi,

Is there any command line tool or method that allow for an easy translation from HGVS to hg19 coordinates?
for example:

as an inptu I'd like to provde: NM_001100.3:c.7G>T and the output...
Forum: Bioinformatics 02-07-2013, 12:18 AM
Replies: 6
Views: 5,745
Posted By thedamian
heh yes, I've just realised it. If starnd is...

heh yes, I've just realised it.
If starnd is "-", start codon is cdsEnd and end codon is cdsStart! Very confusing!
+ 1 to experience:)
Forum: Bioinformatics 02-06-2013, 11:47 PM
Replies: 6
Views: 5,745
Posted By thedamian
ok, real example: I have gene IL10,...

ok, real example:
I have gene IL10, NM_000572.2.
Based on NM_000572 from UCSC I get:

name: NM_000572
chrom: chr1
strand: -
txStart: 206940947
txEnd: 206945839
cdsStart: 206941980
Forum: Bioinformatics 02-05-2013, 11:17 AM
Replies: 6
Views: 5,745
Posted By thedamian
heh, it was an abstract example:) 012345 is like...

heh, it was an abstract example:) 012345 is like abcdef:)
I test ~3000 genes in such way. 1600 works good, they are "+" strand.
~1400 are "-" and when I use samtools faidx, I can't get correct...
Forum: Bioinformatics 02-05-2013, 08:08 AM
Replies: 6
Views: 5,745
Posted By thedamian
UCSC refSeq Gene and hg19 coordinate

Hello,
I have a list of mRNA NM_ numers.
In UCSC, hg19->refGene table, I can get exons and cds coordinates for every NM_.

However, when I pull out a subsequence from hg19 based on refGene...
Forum: Bioinformatics 12-13-2012, 12:25 AM
Replies: 4
Views: 4,519
Posted By thedamian
@GenoMax, do you know if there is any robust way...

@GenoMax, do you know if there is any robust way to download sequences of pseudogenes of the gene?

I have already GBK RefSeqGene sequences and additionaly I'd like to have corresponding...
Showing results 1 to 25 of 49

 


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