Forum: Bioinformatics
08-03-2016, 07:57 AM
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Replies: 1
Views: 1,445
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...
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Forum: Bioinformatics
06-27-2016, 08:59 AM
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Replies: 0
Views: 998
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Forum: Bioinformatics
05-12-2015, 10:53 AM
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Replies: 15
Views: 22,324
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...
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Forum: Bioinformatics
05-12-2015, 03:09 AM
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Replies: 15
Views: 22,324
I believe here:...
I believe here: http://sourceforge.net/projects/picard/files/picard-tools/
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Forum: Bioinformatics
05-12-2015, 02:41 AM
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Replies: 15
Views: 22,324
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 ;)
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Forum: Bioinformatics
10-16-2014, 03:42 AM
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Replies: 1
Views: 1,595
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Forum: Bioinformatics
04-07-2014, 02:26 AM
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Replies: 4
Views: 2,650
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...
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Forum: Bioinformatics
02-21-2014, 07:58 AM
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Replies: 0
Views: 750
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...
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Forum: Bioinformatics
01-21-2014, 05:57 AM
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Replies: 3
Views: 2,676
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Forum: Bioinformatics
01-21-2014, 04:11 AM
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Replies: 3
Views: 2,676
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Forum: Bioinformatics
12-18-2013, 02:51 AM
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Replies: 1
Views: 1,097
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....
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Forum: Bioinformatics
11-12-2013, 05:01 AM
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Replies: 1
Views: 1,136
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?
...
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Forum: Bioinformatics
10-09-2013, 02:06 AM
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Replies: 18
Views: 15,845
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Forum: Bioinformatics
10-07-2013, 02:49 PM
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Replies: 18
Views: 15,845
set these paramaters:...
set these paramaters: http://pokazywarka.pl/1ve6r7/ and then click "get output". Adjust your parameters and then click "get BED".
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Forum: Bioinformatics
09-13-2013, 02:27 AM
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Replies: 13
Views: 18,403
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...
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Forum: Bioinformatics
05-23-2013, 01:54 AM
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Replies: 4
Views: 2,180
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Forum: Bioinformatics
05-22-2013, 01:41 AM
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Replies: 4
Views: 2,180
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Forum: Bioinformatics
05-21-2013, 07:01 AM
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Replies: 4
Views: 2,180
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...
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Forum: Bioinformatics
04-10-2013, 01:44 AM
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Replies: 2
Views: 1,498
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Forum: Bioinformatics
04-09-2013, 07:05 AM
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Replies: 2
Views: 1,498
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...
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Forum: Bioinformatics
02-07-2013, 01:18 AM
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Replies: 6
Views: 5,936
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Forum: Bioinformatics
02-07-2013, 12:47 AM
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Replies: 6
Views: 5,936
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
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Forum: Bioinformatics
02-05-2013, 12:17 PM
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Replies: 6
Views: 5,936
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Forum: Bioinformatics
02-05-2013, 09:08 AM
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Replies: 6
Views: 5,936
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...
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Forum: Bioinformatics
12-13-2012, 01:25 AM
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Replies: 4
Views: 4,788
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