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Forum: Bioinformatics 09-04-2015, 06:15 AM
Replies: 0
Views: 1,231
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 08-25-2015, 05:31 AM
Replies: 5
Views: 2,068
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 06-10-2015, 12:06 AM
Replies: 7
Views: 1,945
Posted By Irina Pulyakhina
Everything is clear now, thanks!

Everything is clear now, thanks!
Forum: Bioinformatics 06-09-2015, 04:25 AM
Replies: 7
Views: 1,945
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 06-09-2015, 04:08 AM
Replies: 7
Views: 1,945
Posted By Irina Pulyakhina
Thanks GenoMax! But this is weird -- your link...

Thanks GenoMax! But this is weird -- your link says they used MapSplice for RNAseq alignment, and this one says they used BWA for RNAseq alignment:
...
Forum: Bioinformatics 06-09-2015, 03:39 AM
Replies: 7
Views: 1,945
Posted By Irina Pulyakhina
Found it: reference for WXS: ->...

Found it:

reference for WXS:
-> http://www.biomedcentral.com/1471-2105/15/247 (in the Methods section)

reference for RNA-Seq:
->...
Forum: Bioinformatics 06-09-2015, 03:32 AM
Replies: 7
Views: 1,945
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 12-24-2014, 05:18 AM
Replies: 2
Views: 2,358
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 11-26-2012, 06:56 AM
Replies: 3
Views: 2,563
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 02-03-2012, 03:32 AM
Replies: 12
Views: 47,526
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 11-02-2011, 06:23 AM
Replies: 1
Views: 6,927
Posted By Irina Pulyakhina
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]...
Forum: Bioinformatics 10-20-2011, 05:31 AM
Replies: 2
Views: 7,733
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 10-19-2011, 03:03 AM
Replies: 4
Views: 26,234
Posted By Irina Pulyakhina
Thank you! Do you know whether I can get total...

Thank you! Do you know whether I can get total number of mapped reads anyhow with samtools?
Forum: Bioinformatics 10-18-2011, 09:57 AM
Replies: 4
Views: 26,234
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 10-06-2011, 08:16 AM
Replies: 15
Views: 7,254
Posted By Irina Pulyakhina
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...
Forum: RNA Sequencing 09-27-2011, 03:33 AM
Replies: 10
Views: 8,490
Posted By Irina Pulyakhina
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...
Forum: RNA Sequencing 09-27-2011, 02:09 AM
Replies: 4
Views: 2,690
Posted By Irina Pulyakhina
Yes, I've just sent it, the email "MapSplice logs...

Yes, I've just sent it, the email "MapSplice logs directory" to griff@netlab.uky.edu (just netlab.uky.edu didn't work). Thank again!
Forum: RNA Sequencing 09-25-2011, 10:12 PM
Replies: 4
Views: 2,690
Posted By Irina Pulyakhina
Thank you for your reply! I found out the problem...

Thank you for your reply! I found out the problem and MapSplice is passing through this point no, but I do get the other error:

=======================
Warning: Empty input file
Error: No...
Forum: RNA Sequencing 09-15-2011, 01:31 AM
Replies: 4
Views: 2,690
Posted By Irina Pulyakhina
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...
Forum: RNA Sequencing 09-14-2011, 01:52 AM
Replies: 0
Views: 1,290
Posted By Irina Pulyakhina
hmmSplicer

Good morning everyone,

Do you know whether hmmSplicer can work with Illumina paired-end sequencing data?

Thanks in advance,
Irina
Forum: Bioinformatics 08-15-2011, 02:24 AM
Replies: 0
Views: 1,664
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 08-15-2011, 01:41 AM
Replies: 1
Views: 2,243
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 08-15-2011, 01:39 AM
Replies: 0
Views: 1,226
Posted By Irina Pulyakhina
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...
Forum: Bioinformatics 09-21-2010, 03:31 AM
Replies: 0
Views: 2,360
Posted By Irina Pulyakhina
Helicos: "dark nucleotides" and the coverage parameter

Dear Mosaik users,

I'm quit new to this program. I work with the Helicos data so it's crucial for me to know the following: aligning the Helicos data to the reference genome sequence, does Mosaik...
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