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Search: Posts Made By: tdoniger
Forum: Bioinformatics 01-15-2014, 08:53 AM
Replies: 0
Views: 1,188
Posted By tdoniger
pybedtools- merge

Hi,
I wrote a script that looks takes random subsets from a bed file and merges them and sees how many unique loci are in the subset. I want to now see in each subset - how many loci there are that...
Forum: Bioinformatics 07-10-2013, 06:19 AM
Replies: 6
Views: 3,420
Posted By tdoniger
quite a bit. very little starting material

quite a bit. very little starting material
Forum: Bioinformatics 07-10-2013, 05:57 AM
Replies: 6
Views: 3,420
Posted By tdoniger
Hi, Thanks! But I was trying to explain that...

Hi,

Thanks! But I was trying to explain that I managed to solve it. I had thought that every line marked by "PG:Z:MarkDuplicates" was a duplicate, but really this was not the case. The duplicates...
Forum: Bioinformatics 07-09-2013, 02:12 AM
Replies: 6
Views: 3,420
Posted By tdoniger
I thought because every line contained: ...

I thought because every line contained: PG:Z:MarkDuplicates - that these were the reads marked as duplicates. This is not the case. It is the flag set in the second column that indicates whether it...
Forum: Bioinformatics 02-14-2013, 01:48 AM
Replies: 6
Views: 3,420
Posted By tdoniger
Picard MarkDuplicates - whole bam file marked as duplicates

Hi,

I ran an RNA-Seq data set using the RUM-pipeline to align the data. I tried to use the Picard's MarkDuplicates - and it tagged very single read in the bam files as a duplicate.
I used the...
Forum: Bioinformatics 07-11-2012, 12:42 AM
Replies: 3
Views: 2,671
Posted By tdoniger
Finishing a de novo assembly of bacteria genome from single-end reads

I have assembled a ~5Mb bacterial genome using both Edena and CLC Bio. I have about several hundred contigs.

The lab is willing to sequence to close up some of the gaps - about 50...but not 500....
Forum: RNA Sequencing 02-29-2012, 03:00 AM
Replies: 0
Views: 1,285
Posted By tdoniger
Digital Gene Expression - raw read counts

I apologize if an existing answer to the following question has already been addressed in this forum.

I am analyzing solexa either 35 or 75 bp single-end reads.

If I understand correctly,...
Forum: Bioinformatics 03-15-2011, 07:22 AM
Replies: 5
Views: 8,795
Posted By tdoniger
Thank you. What concerns me is that some of...

Thank you.

What concerns me is that some of the alignments returned in the original bowtie file disappeared when I ran bowtie2sam.pl

If I understand correctly now---the script bowtie2sam.pl...
Forum: Bioinformatics 03-15-2011, 04:35 AM
Replies: 5
Views: 8,795
Posted By tdoniger
Convert from bowtie to sam

Hi,

I used samtools- bowtie2sam.pl to convert a bowtie file to a sam file. Later, I noticed that some of the alignments were missing in the sam file. Is this expected? Is there another bowtie to...
Forum: Bioinformatics 02-08-2011, 11:29 PM
Replies: 3
Views: 6,281
Posted By tdoniger
Wow! Thank you! Just what I was looking for! The...

Wow! Thank you! Just what I was looking for! The 'cln2qual' tool works great. I didn't notice it in the SeqClean directory. Newbler accepts the input without any problems.

Thanks again,
Tirza
Forum: Bioinformatics 02-08-2011, 12:08 AM
Replies: 3
Views: 6,281
Posted By tdoniger
Vector Removal Software

I am trying to perform de novo assembly on 454 data using Newbler v2.5.

As a first stage, I need to remove the vector sequence. I have the vector sequence.

1. Using newbler, I have included...
Forum: Bioinformatics 12-29-2010, 01:36 AM
Replies: 4
Views: 3,079
Posted By tdoniger
Fastxtoolkit nucleotide distribution issue

Hi,

I don't know if it is correct, but I just commented out the lines of the file check from the shell file and it works without any problem.

Good luck!
Tirza
Forum: Introductions 11-14-2010, 05:23 AM
Replies: 373
Views: 151,064
Posted By tdoniger
Hi

Hi,

I am work in the Bioinformatics Unit at Bar Ilan University,Israel. Most of our users have sequenced their data using illumina. I am fairly new to next generation sequencing and greatly...
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