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Forum: Bioinformatics 08-02-2014, 10:45 AM
Replies: 17
Views: 5,543
Posted By Genomics101
Thanks, Brian. This is where I am showing my...

Thanks, Brian. This is where I am showing my ignorance I am sure, but how did the reads become so short? Looking at what I pulled out of the sam file, they are full-length (300bp) reads for the...
Forum: Bioinformatics 08-02-2014, 10:21 AM
Replies: 17
Views: 5,543
Posted By Genomics101
Thanks very much, GenoMax. Indeed, it is MiSeq...

Thanks very much, GenoMax. Indeed, it is MiSeq data, but I never had this problem with MiSeq before (that was with 250bp PE reads, these are 300s). Can you tell me more the particular pathology...
Forum: Bioinformatics 08-02-2014, 08:52 AM
Replies: 17
Views: 5,543
Posted By Genomics101
A million thanks Brian, I have been puzzling over...

A million thanks Brian, I have been puzzling over this for days and with your help it was unraveled in just some hours. The key was looking for the reads with >2 placements, how did you know? Do you...
Forum: Bioinformatics 08-01-2014, 07:02 PM
Replies: 17
Views: 5,543
Posted By Genomics101
Removed all reads less that 200bp and quality...

Removed all reads less that 200bp and quality under 20 and viola:
http://i.imgur.com/LRdTYIg.png
Forum: Bioinformatics 08-01-2014, 06:17 PM
Replies: 17
Views: 5,543
Posted By Genomics101
Yes I am using BWA (MEM). Here is a read...

Yes I am using BWA (MEM).

Here is a read whose name shows up 8 times:

M01243:91:000000000-A6ELJ:1:2119:9911:4339 65 Pf3D7_14_v3 2584936 49 63M1D87M150S = 2584936 0 ...
Forum: Bioinformatics 08-01-2014, 05:44 PM
Replies: 17
Views: 5,543
Posted By Genomics101
Hi, Brian. I'm doing that now. In the mean...

Hi, Brian. I'm doing that now. In the mean time, here is how it looks with reads that only have unique positions: http://i.imgur.com/zNLG0ey.png

Although I didn't trim the reads I noticed that...
Forum: Bioinformatics 08-01-2014, 03:18 PM
Replies: 17
Views: 5,543
Posted By Genomics101
The mystery continues. I did all the analyses...

The mystery continues. I did all the analyses again with exactly the same results. Filtering for the primary alignments however gives me MORE reads in total than i have with just the original FASTQ...
Forum: Bioinformatics 08-01-2014, 01:20 PM
Replies: 17
Views: 5,543
Posted By Genomics101
This is true and and I puzzled by it as well. ...

This is true and and I puzzled by it as well. Although the number of reads went down after I extracted only the mapped reads (or so I thought), not enough. I'm going to make sure I am doing things...
Forum: Bioinformatics 08-01-2014, 12:42 PM
Replies: 17
Views: 5,543
Posted By Genomics101
Hi, Brian, thanks for your response. ...

Hi, Brian, thanks for your response.



This is not the case, the number or reads went from 1804074 total to 1801608 after filtering for unmapped reads. The maximum number on the Y-axis is...
Forum: Bioinformatics 08-01-2014, 11:56 AM
Replies: 17
Views: 5,543
Posted By Genomics101
Bizarre per sequence GC content distribution, what could cause this?

Greetings. I am working with an Illumina library of whole genome sequence for a very AT-rich genome. When I initially did a FASTQC I saw this: http://imgur.com/eVda7tD.png

The bimodal...
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