Tweet
I have a big problem about s_N_export profile.
My boss tell me that his all sequencing profiles are single read.
However, the 8th column in the s_N_export profile all are 1 (1 or 2 for paired-read analysis, blank for a single-read analysis).
What is happen?
The s_N_export profile format below:
Not all fields are relevant to a single-read analysis.
1. Machine (Parsed from Run Folder name)
2. Run Number (Parsed from Run Folder name)
3. Lane
4. Tile
5. X Coordinate of cluster
6. Y Coordinate of cluster
7. Index string (Bland for a non-indexed run)
8. Read number (1 or 2 for paired-read analysis, blank for a single-read analysis)
9. Read
10.Quality string—In symbolic ASCII format (ASCII character code = quality value + 64)
by default (Set QUALITY_FORMAT --numeric in theGERALD config file for numeric
values)
11. Match chromosome—Name of chromosome match OR code indicating why no
match resulted
12. Match Contig—Gives the contig name if there is a match and the match
chromosome is split into contigs (Blank if no match found)
13. Match Position—Always with respect to forward strand, numbering starts at 1 (Blank
if no match found)
14. Match Strand—“F” for forward, “R” for reverse (Blank if no match found)
15. Match Descriptor—Concise description of alignment (Blank if no match found)
• A numeral denotes a run of matching bases
• A letter denotes substitution of a nucleotide:
For a 35 base read, “35” denotes an exact match and “32C2” denotes substitution
of a “C” at the 33rd position
16. Single-Read Alignment Score—Alignment score of a single-read match, or for a
paired read, alignment score of a read if it were treated as a single read (Blank if no
match found)
17. Paired-Read Alignment Score—Alignment score of a paired read and its partner,
taken as a pair (Blank for single-read analysis)
18. Partner Chromosome—Name of the chromosome if the read is paired and its partner
aligns to another chromosome (Blank for single-read analysis)
19. Partner Contig—Not blank if read is paired and its partner aligns to another
chromosome and that partner is split into contigs (Blank for single-read analysis)
20. Partner Offset—If a partner of a paired read aligns to the same chromosome and
contig, this number, added to the Match Position, gives the alignment position of the
partner (Blank for single-read analysis)
21. Partner Strand—To which strand did the partner of the paired read align? “F” for
forward, “R” for reverse (Blank if no match found, blank for single-read analysis)
22. Filtering—Did the read pass quality filtering? “Y” for yes, “N” for no
My boss tell me that his all sequencing profiles are single read.
However, the 8th column in the s_N_export profile all are 1 (1 or 2 for paired-read analysis, blank for a single-read analysis).
What is happen?
The s_N_export profile format below:
Not all fields are relevant to a single-read analysis.
1. Machine (Parsed from Run Folder name)
2. Run Number (Parsed from Run Folder name)
3. Lane
4. Tile
5. X Coordinate of cluster
6. Y Coordinate of cluster
7. Index string (Bland for a non-indexed run)
8. Read number (1 or 2 for paired-read analysis, blank for a single-read analysis)
9. Read
10.Quality string—In symbolic ASCII format (ASCII character code = quality value + 64)
by default (Set QUALITY_FORMAT --numeric in theGERALD config file for numeric
values)
11. Match chromosome—Name of chromosome match OR code indicating why no
match resulted
12. Match Contig—Gives the contig name if there is a match and the match
chromosome is split into contigs (Blank if no match found)
13. Match Position—Always with respect to forward strand, numbering starts at 1 (Blank
if no match found)
14. Match Strand—“F” for forward, “R” for reverse (Blank if no match found)
15. Match Descriptor—Concise description of alignment (Blank if no match found)
• A numeral denotes a run of matching bases
• A letter denotes substitution of a nucleotide:
For a 35 base read, “35” denotes an exact match and “32C2” denotes substitution
of a “C” at the 33rd position
16. Single-Read Alignment Score—Alignment score of a single-read match, or for a
paired read, alignment score of a read if it were treated as a single read (Blank if no
match found)
17. Paired-Read Alignment Score—Alignment score of a paired read and its partner,
taken as a pair (Blank for single-read analysis)
18. Partner Chromosome—Name of the chromosome if the read is paired and its partner
aligns to another chromosome (Blank for single-read analysis)
19. Partner Contig—Not blank if read is paired and its partner aligns to another
chromosome and that partner is split into contigs (Blank for single-read analysis)
20. Partner Offset—If a partner of a paired read aligns to the same chromosome and
contig, this number, added to the Match Position, gives the alignment position of the
partner (Blank for single-read analysis)
21. Partner Strand—To which strand did the partner of the paired read align? “F” for
forward, “R” for reverse (Blank if no match found, blank for single-read analysis)
22. Filtering—Did the read pass quality filtering? “Y” for yes, “N” for no
Comment