I have used 100 nt paired-end sequences to construct a reduced representation reference genome of the organism I am working with. I aligned the reads back to the reference genome. I hope to find SNPs at some point. I have a list of individual reads (with the paired read) which I would like to inspect in the alignment. Is there a way to find out what position in the reference genome these reads are aligned to? I can visualize the aligned reads in IGV and there I can zoom in to a position to inspect a region. But I cannot search for a particular read - I need to know the map position of the read first. Is there a programme of script that could extract the position (and maybe other infrmation) of an individual read from a sam/bam file?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Tablet lets you search for reads by name, the regular expression support is also very handy: http://bioinf.hutton.ac.uk/tablet/
Comment
-
Originally posted by dpryan View PostPresumably you have the SAM file that was output from the aligner. You can look for the location of a read in it using grep: grep -m 1 -w SomeReadName.123455 Aligned.sam
That'll be easy enough provided you only have a few reads you want to look at,
Thanks for the suggestion. However, when I use the command grep -m 1 Sequence_read_tag alignment_file.sam > output.txt
I get the following information:
FCB020AACXX:6:1305:20474:84915#ATGAACCT 163 369552-8 1 60 100M = 61 160 CTTGCAAAGGAAAATCTTGAGATGAACGAGGGCGACATTAGCAAGGAGGCCATCGGAGGCACCGACGGTACCACCGTCGATGGAGAGGATGCGAACCCAT bbbeeeeeggggfiiiiiiiihgifhihffhiiiiihiihiihfghfhiihggggeeecccccccccc]acccccc_acacccccccccccccccccccc XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:100
I recognize the name of my sequence, the sequence itself, the quality information... but where do I find the positional information?
Comment
-
Originally posted by maubp View PostTablet lets you search for reads by name, the regular expression support is also very handy: http://bioinf.hutton.ac.uk/tablet/
Comment
-
Originally posted by Tectona View PostThanks for the suggestion. However, when I use the command grep -m 1 Sequence_read_tag alignment_file.sam > output.txt
I get the following information:
FCB020AACXX:6:1305:20474:84915#ATGAACCT 163 369552-8 1 60 100M = 61 160 CTTGCAAAGGAAAATCTTGAGATGAACGAGGGCGACATTAGCAAGGAGGCCATCGGAGGCACCGACGGTACCACCGTCGATGGAGAGGATGCGAACCCAT bbbeeeeeggggfiiiiiiiihgifhihffhiiiiihiihiihfghfhiihggggeeecccccccccc]acccccc_acacccccccccccccccccccc XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:100
I recognize the name of my sequence, the sequence itself, the quality information... but where do I find the positional information?
Code:grep -m 1 Sequence_read_tag alignment_file.sam | awk '{ print $3":"$4 }' > output.txt
Comment
-
That's position according to the reference contig it's aligned against. You may want to browse the SAM specification. The read you showed maps to the start of a contig.
Comment
Latest Articles
Collapse
-
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 -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment