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Search: Posts Made By: litali
Forum: Bioinformatics 11-07-2015, 07:14 AM
Replies: 0
Views: 552
Posted By litali
annotation for 454 mapper

is it possible in the 454 mapper to receive annotations for bacteria or is it possible only with the ucsc human annotation files?
Forum: Bioinformatics 10-12-2015, 04:27 AM
Replies: 13
Views: 1,236
Posted By litali
transcript

exactly, I think one of the transcripts is the dominant form, I just wonder how one can know which one is the dominant?
Forum: Bioinformatics 10-12-2015, 03:42 AM
Replies: 13
Views: 1,236
Posted By litali
I am working on human, in the gene i am working...

I am working on human, in the gene i am working on there are several transcripts, and there is more than one which is protein coding, but all the work in the litareature relates only to one of them....
Forum: Bioinformatics 10-12-2015, 03:23 AM
Replies: 13
Views: 1,236
Posted By litali
transcripts ensembl

but where can i found this information? in the ensembl I only see the list of the transcripts. However, in articles in the literature usually only one of the transcripts is adressed
Forum: Bioinformatics 10-12-2015, 02:53 AM
Replies: 13
Views: 1,236
Posted By litali
which is the main transcript

For a specific gene, how can I know which is the main transcript in the ensembl? there is a list of few transcripts and not always the first one or the longest one is the one which is considered the...
Forum: Bioinformatics 10-06-2015, 04:00 AM
Replies: 0
Views: 757
Posted By litali
error unable to parse known snp

I try to use 454 mapper with the SNP file from ucsc.
it begins the mapping but then there is an erroe:
" unable to parse known snps file."
How this can be solved?
Forum: Bioinformatics 08-06-2015, 12:40 AM
Replies: 0
Views: 476
Posted By litali
displaying 454 data on ucsc

How can i display the 454.bam file on the ucsc custom tracks?
I have the contigs.bam file from the 454mapper software. Thare is no index file which seems to be required to the ucsc..
Forum: Bioinformatics 10-24-2013, 02:24 AM
Replies: 7
Views: 2,889
Posted By litali
qiime forum

I found how to post there, thank you
Forum: Bioinformatics 10-24-2013, 02:16 AM
Replies: 7
Views: 2,889
Posted By litali
qiime forum

I tried to use the qiime forum, but I son't see where can I post a new message there,,,
Forum: Bioinformatics 10-24-2013, 01:24 AM
Replies: 7
Views: 2,889
Posted By litali
16s some qiime questions

I have 0ne 16s sample (without barcodes, as this is only one sample) sequenced by 454. I want to use qiime to analyze it:
1. Which step do I need to start from ? It is only one sample so do I need...
Forum: Bioinformatics 10-23-2013, 03:19 AM
Replies: 5
Views: 1,249
Posted By litali
qiime for one sample

In previous response Ciaran suggested that I should start the pipeline from the step post demultiplexing, tha's why I asked that if I start post demultiplexing, I actually start with the Pick otus...
Forum: Bioinformatics 10-23-2013, 02:51 AM
Replies: 5
Views: 1,249
Posted By litali
qiime for one sample

but if I skip the demultiplexing step how will the linkerprimer be removed? I understand that it is the demultiplexing step that usually performs it..
Forum: Bioinformatics 10-23-2013, 01:18 AM
Replies: 5
Views: 1,249
Posted By litali
16s analysis for one sample

How can I perform an analysis for one sample 454 16s sequences?
I thought to use qiime, but there are steps relating to the barcodes. I don't have barcodes in my sequences, only primers.
Forum: Bioinformatics 11-14-2012, 02:41 AM
Replies: 0
Views: 581
Posted By litali
454 newbler mapper annotation for non human

Hi,
I wanted to know whether it is possible to receive in newbler mapper annotation of genes and SNP for organism which are not in the ucsc, such as e. coli
Thank you!
Forum: Bioinformatics 08-31-2012, 12:13 AM
Replies: 1
Views: 744
Posted By litali
assembly and strand definition

When a novel genome is assembled into a contig, how is it defined whether the contig is the
+ or the - strand? the complement strand could have been assembled instead?
Forum: Bioinformatics 08-21-2012, 03:49 AM
Replies: 6
Views: 1,687
Posted By litali
clc or dnastar

Hi,
Which software is more recommended for NGS analysis, array analysis, probes and primers etc, CLC or DNASTAR?
Forum: Bioinformatics 08-19-2012, 10:37 PM
Replies: 1
Views: 1,476
Posted By litali
OTU 16s 454

Hi, What software is recommended for analyzing 454 16s data for OTU analysis?
Forum: Bioinformatics 10-23-2011, 01:18 AM
Replies: 2
Views: 1,602
Posted By litali
removing mids

Hi
I want to separate the sequences according to the different mids and then to trim the mids, but those are "home made" mids (we planned them), and not the 454 mids. Is it possible via the sff...
Forum: Bioinformatics 09-22-2011, 01:38 AM
Replies: 36
Views: 4,392
Posted By litali
Thank you all for your help! jkbonfield, I got...

Thank you all for your help!
jkbonfield, I got this error "No M or N operator between pair of I operators in CIGAR" in picard for all the reads..
Forum: Bioinformatics 09-21-2011, 11:52 PM
Replies: 36
Views: 4,392
Posted By litali
I found hoe to see the bases, thanx!! another...

I found hoe to see the bases, thanx!! another question: what does it mean the "cigar" line with a number following it?
and also is it possible to use noe this sorted bam file to upload it to ucsc...
Forum: Bioinformatics 09-21-2011, 11:45 PM
Replies: 36
Views: 4,392
Posted By litali
Bam

Thank you alot!
I now can see the akignments in IGV. However, I think I only see the coverage. how can I see the SNPs or the reads themselves? I now see where the reads are mapped, but it is just...
Forum: Bioinformatics 09-21-2011, 10:51 PM
Replies: 36
Views: 4,392
Posted By litali
Bam

ok, i installed the newer version of samtools, so idxstats gives the following:
chrX 154913754 47196 0
* 0 0 0

I also attach a few more reads from the first lines of...
Forum: Bioinformatics 09-21-2011, 04:30 AM
Replies: 36
Views: 4,392
Posted By litali
samtools, igv and more

when i try samtools idxstats, I receive command not found. indeed in the help menu of samtools which I installed I have only:
Program: samtools (Tools for alignments in the SAM format)
Version:...
Forum: Bioinformatics 09-21-2011, 03:46 AM
Replies: 36
Views: 4,392
Posted By litali
IGv

it says: " loading SAM/BAM index files is not supported ....sorted.bam.bai..Load the SAM/ BAM files directly"
When I click "ok" it says "xoom in to see the alignments" but even if I soom in, it is...
Forum: Bioinformatics 09-21-2011, 03:14 AM
Replies: 36
Views: 4,392
Posted By litali
Igv

ok, I installed samtools and created the sorted and the index files. Now I tried to upload them into the IGV viewer, but still I see no alignments..
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