Editing
Matt:LabNotes/2013-8-23
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
==Novoalign to repeat alignment of End Sequencing reads== *Build index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex [options] [indexfile] [sequencefiles] *Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign [options] **/home/kunzhang/softwares/Novocraft/novocraft/novoalign -d [indexfile] -f [readsfile] -F [readsfileformat] -r [reads_to_report] -o [outputfileformat] > [outputfile] ***Readsfileformat: FA - fasta; ILMFQ - Illumina1.3+ Phred+64; STDFQ - Sanger Phred+33; SLXFQ - Solexa+64 ===CA12k=== Build index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex /home/mzcai/CA12k_EndSequencing_Analysis/Novoalign/CAprobes_50bp.ndx /home/mzcai/CA12k_EndSequencing_Analysis/CAprobes_to_order_50bp.fa<br> Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/mzcai/CA12k_EndSequencing_Analysis/Novoalign/CAprobes_50bp.ndx -f /home/mzcai/CA12k_EndSequencing_Analysis/s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM > Readsalign2probes_CA_novoalign.sam # Read Sequences: 29716630 # Aligned: 6607495 # Unique Alignment: 6586488 # Gapped Alignment: 2219484 # Quality Filter: 146500 # Homopolymer Filter: 758 # Elapsed Time: 13736.789 (sec.) # CPU Time: 225.9 (min.) # Done at Fri Aug 23 15:56:01 2013 *This does a local alignment so CIGAR string contains 'S', which stands for soft-clipping **I want to avoid that since it will remove some of the synthesis errors we are trying to measure **Use -o FULLNW to do end-to-end alignment ===Agi26k0gap=== Build Index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k0gapprobes.ndx /home/mzcai/Agi26k_EndSequencing_Analysis/Agi26k0gap_corrected.fa Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k0gapprobes.ndx -f /home/mzcai/Agi26k_EndSequencing_Analysis/s_3_1_Indx10.txt -F ILMFQ -r ALL -o SAM > /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Readsalign2probes_Agi26k0gap_novoalign.sam 2> /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/0gapstderr.txt & # Read Sequences: 16368416 # Aligned: 6005917 # Unique Alignment: 6004799 # Gapped Alignment: 1727168 # Quality Filter: 56701 # Homopolymer Filter: 9 # Elapsed Time: 13633.364 (sec.) # CPU Time: 171.2 (min.) # Done at Fri Aug 23 20:32:11 201 ===Agi26k20gap=== Build Index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k20gapprobes.ndx /home/mzcai/Agi26k_EndSequencing_Analysis/Agi26k20gap_corrected.fa Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k20gapprobes.ndx -f /home/mzcai/Agi26k_EndSequencing_Analysis/s_3_1_Indx12.txt -F ILMFQ -r ALL -o SAM > /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Readsalign2probes_Agi26k20gap_novoalign.sam 2> /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/20gapstderr.txt & # Read Sequences: 17308686 # Aligned: 4798906 # Unique Alignment: 4794645 # Gapped Alignment: 1353496 # Quality Filter: 48231 # Homopolymer Filter: 10 # Elapsed Time: 14327.598 (sec.) # CPU Time: 180.0 (min.) # Done at Fri Aug 23 20:47:56 2013
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information