I am new to bioinformatics and I just starting working on two datasets in an attempt to identify allele-specific expression. I currently am working on Galaxy until I get a new workstation/server access.
So far I have 2 BAM files, which were mapped with Tophot, that I am working with to call SNPs. I used samtools to sort both files, and tried to run mpileup locally (but got a segmentation fault). When I run mpileup on Galaxy using the unsorted files, I get output files that are approximately 100GB per BAM file. When I look at the data, there seems to be no chromosome information (reads chrM).
To troubleshoot, I took a small part of one of the BAM files and ran mpileup locally and filtered the output and the data appeared to be what I wanted (ex. chr1 64179067 A A 75 75 25 23 ., II).
Is a 100GB output file normal? Are there steps that I am missing as far as filtering the BAM prior to mpileup?
Note the starting BAM files are 6GB and 5GB.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
27 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
30 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|