Forum: Bioinformatics
09-04-2015, 06:15 AM
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Replies: 0
Views: 1,231
almost no hits when mapping against miRBase
Hi guys,
I'm trying to map human miRNA data (Illumina 2500, ~22bp reads, adapters already trimmed) to the most recent release of microRNA database, miRBase (hairpin miRNA and mature miRNA). I'm...
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Forum: Bioinformatics
08-25-2015, 05:31 AM
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Replies: 5
Views: 2,068
mapping microRNA data -- less than 1% maps
Hi guys,
I am not new to NGS/RNA-Seq, but I am new to miRNA sequencing... I want to map human miRNA reads (HiSeq 2500, single end, 50bp) to the miRNA databases (mature and hairpin, I took both...
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Forum: Bioinformatics
06-10-2015, 12:06 AM
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Replies: 7
Views: 1,945
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Forum: Bioinformatics
06-09-2015, 04:25 AM
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Replies: 7
Views: 1,945
I am looking at level 2 data (I am doing my...
I am looking at level 2 data (I am doing my analysis on the bam files directly), but I would think that bam files generated at level 2 would be used for all the calculations at level 3, wouldn't this...
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Forum: Bioinformatics
06-09-2015, 04:08 AM
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Replies: 7
Views: 1,945
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Forum: Bioinformatics
06-09-2015, 03:39 AM
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Replies: 7
Views: 1,945
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Forum: Bioinformatics
06-09-2015, 03:32 AM
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Replies: 7
Views: 1,945
TCGA data aligner
Hi everyone,
Does anyone know what aligner was used for the TCGA data (could not find this info on the amazingly "handy" website, feels like they are trying to hide it)? I am interested in the...
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Forum: Bioinformatics
12-24-2014, 05:18 AM
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Replies: 2
Views: 2,358
Varscan output contains dots
Hi guys,
I'm using VarScan v 2.3.7 to call SNPs in Illumina Hiseq2000 RNA-Seq paired-end sample:
> samtools mpileup -B -Q 0 -f reference.fa $CONTROL.bam > sample.mpileup
> java -jar VarScan...
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Forum: Bioinformatics
11-26-2012, 06:56 AM
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Replies: 3
Views: 2,563
VarScan for heterozygous calls
Dear all,
I'm running VarScan:
java -jar ./VarScan.v2.2.8.jar mpileup2snp --min-var-freq 0.1 --output-vcf --variants input.mpileup
And I get two output files, with SNPs and indels. I have...
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Forum: Bioinformatics
02-03-2012, 03:32 AM
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Replies: 12
Views: 47,526
Hi all,
Does anyone know the difference...
Hi all,
Does anyone know the difference between N and D in CIGAR? I assume for long deletions (let's say 1000 b.p.) you'll get "1000N" and for short ones (let's say 2 b.p.) you'll get "2D" in the...
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Forum: Bioinformatics
11-02-2011, 06:23 AM
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Replies: 1
Views: 6,927
samtools sam file no headers
Dear all,
I have the following problem: my sam file contain no headers, so I can't convert it to bam directly, I get the following error:
> samtools view -S accepted_hits.sam
The tag [ID]...
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Forum: Bioinformatics
10-20-2011, 05:31 AM
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Replies: 2
Views: 7,733
What kind of aligner do you use? You have...
What kind of aligner do you use? You have paired-end data, so you can have your mate pairs aligned as pairs (and this is the proper way) --> this is number in line 5, or independently --> and is...
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Forum: Bioinformatics
10-19-2011, 03:03 AM
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Replies: 4
Views: 26,234
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Forum: Bioinformatics
10-18-2011, 09:57 AM
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Replies: 4
Views: 26,234
samtools idxstats
Dear all,
With this command:
samtools idxstats aln.sorted.bam
You get a TAB delimited output where each line consists of ref.seq. name, ref.seq. length, number of mapped reads and number of...
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Forum: Bioinformatics
10-06-2011, 08:16 AM
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Replies: 15
Views: 7,254
Trimmomatic error while executing
Hi everyone,
I'm trying to run Trimmomatic v0.15. I'm working with Illumina paired end data. With this command:
java -classpath ./trimmomatic.jar org.usadellab.trimmomatic.TrimmomaticSE...
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Forum: RNA Sequencing
09-27-2011, 03:33 AM
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Replies: 10
Views: 8,490
GMAP gsnap input error
Hi everyone,
I'm trying to run gsnap programm with paired-end Illumina data. This is the command:
gsnap -D /data/database -d hg19 s_5.1.fastq .s_5.2.fastq -A sam >> s_5__hg19.sam
After two...
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Forum: RNA Sequencing
09-27-2011, 02:09 AM
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Replies: 4
Views: 2,690
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Forum: RNA Sequencing
09-25-2011, 10:12 PM
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Replies: 4
Views: 2,690
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Forum: RNA Sequencing
09-15-2011, 01:31 AM
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Replies: 4
Views: 2,690
MapSplice 1.15.1 error
Hi everyone,
I'm running MapSplice 1.15.1 and get an error:
[Thu Sep 15 11:19:36 2011] Preparing output location /home/ipulyakhina/Programs/MapSplice_1.15.2/RESULTS//
[Thu Sep 15 11:19:36...
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Forum: RNA Sequencing
09-14-2011, 01:52 AM
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Replies: 0
Views: 1,290
hmmSplicer
Good morning everyone,
Do you know whether hmmSplicer can work with Illumina paired-end sequencing data?
Thanks in advance,
Irina
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Forum: Bioinformatics
08-15-2011, 02:24 AM
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Replies: 0
Views: 1,664
TopHat 1.3.1 coverage islands
Dear all,
While TopHat searches for introns, it scans the so-called "coverage islands". Does anyone know what is the coverage cutoff for a region to become such island and also can this cutoff be...
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Forum: Bioinformatics
08-15-2011, 01:41 AM
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Replies: 1
Views: 2,243
TopHat 1.3.1 non-canonical splice junctions
Dear all,
Does anyone know how to control the non-canonical splice sites search? The article says it doesn't search for the non-canonical splice sites but with my data I can see it does. So does...
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Forum: Bioinformatics
08-15-2011, 01:39 AM
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Replies: 0
Views: 1,226
TopHat 1.3.1 butterfly
Hi everyone,
Does anyone know how the following TopHat setting "--butterfly-search" works? The description says it is a slower but potentially more sensitive algorithm to find junctions in...
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Forum: Bioinformatics
09-21-2010, 03:31 AM
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Replies: 0
Views: 2,360
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