This might be a silly question but it is bugging me and I need the answer. I have a set of paired end FASTQ files that contain about 30 million reads total. After aligning them with BWA and sorting the output with samtools, the resulting BAM file now has about 72 million reads. Why????
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Both come from iterating the files in Python. The FASTQ files are read in in blocks of four lines each which is one read. This example is a MiSeq run so 30 million (15 million in each FASTQ) seems realistic. The BAM count is from
bamfile = pysam.AlignmentFile(o['bamfile'], "rb")
bamfile.count()
or
bamfile_reads = functools.reduce(lambda x, y: x + y, [eval('+'.join(l.rstrip('\n').split('\t')[2:])) for l in pysam.idxstats(o['bamfile'])])
or simply counting the reads as I iterate the BAM file to do my analysis.Last edited by pkMyt1; 05-12-2015, 08:36 AM.
Comment
-
Originally posted by Brian Bushnell View PostThat depends on the goal of your experiment. What are you trying to do?
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment