Forum: Bioinformatics
01-15-2014, 08:53 AM
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Replies: 0
Views: 1,188
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...
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Forum: Bioinformatics
07-10-2013, 06:19 AM
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Replies: 6
Views: 3,420
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Forum: Bioinformatics
07-10-2013, 05:57 AM
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Replies: 6
Views: 3,420
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...
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Forum: Bioinformatics
07-09-2013, 02:12 AM
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Replies: 6
Views: 3,420
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...
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Forum: Bioinformatics
02-14-2013, 01:48 AM
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Replies: 6
Views: 3,420
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Forum: Bioinformatics
07-11-2012, 12:42 AM
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Replies: 3
Views: 2,671
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Forum: RNA Sequencing
02-29-2012, 03:00 AM
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Replies: 0
Views: 1,285
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,...
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Forum: Bioinformatics
03-15-2011, 07:22 AM
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Replies: 5
Views: 8,795
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...
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Forum: Bioinformatics
03-15-2011, 04:35 AM
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Replies: 5
Views: 8,795
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...
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Forum: Bioinformatics
02-08-2011, 11:29 PM
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Replies: 3
Views: 6,281
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Forum: Bioinformatics
02-08-2011, 12:08 AM
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Replies: 3
Views: 6,281
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...
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Forum: Bioinformatics
12-29-2010, 01:36 AM
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Replies: 4
Views: 3,079
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Forum: Introductions
11-14-2010, 05:23 AM
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Replies: 373
Views: 151,064
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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