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</head><body bgcolor="#FFFFFF" text="#000000"><span style="font-family:
Helvetica,Arial,sans-serif;">Dear Erich,</span><br style="font-family:
Helvetica,Arial,sans-serif;">
<br style="font-family: Helvetica,Arial,sans-serif;">
<span style="font-family: Helvetica,Arial,sans-serif;">you can indeed do
whatever you like there. However, as I tried to indicate, it might
really make sense to go with -1, -2 or /1, /2.</span><br
style="font-family: Helvetica,Arial,sans-serif;">
<span style="font-family: Helvetica,Arial,sans-serif;">My guess is that a
lot of scripts </span><span style="text-decoration: underline;
font-family: Helvetica,Arial,sans-serif;">could</span><span
style="font-family: Helvetica,Arial,sans-serif;"> struggle with the "#"
you are using.</span><br style="font-family:
Helvetica,Arial,sans-serif;">
<span style="font-family: Helvetica,Arial,sans-serif;">Meanwhile it is
also possible to just "repair" the reads in the .keep file by comparison
with the raw reads file where headers have been fixed. Might save some
time....</span><br style="font-family: Helvetica,Arial,sans-serif;">
<br style="font-family: Helvetica,Arial,sans-serif;">
<span style="font-family: Helvetica,Arial,sans-serif;">Good luck</span><br
style="font-family: Helvetica,Arial,sans-serif;">
<br style="font-family: Helvetica,Arial,sans-serif;">
<span style="font-family: Helvetica,Arial,sans-serif;">Philipp</span><br>
<br>
<blockquote style="border: 0px none;"
cite="mid:202F8B29-DB9A-4BA7-A125-A5D2CE55A57E@cornell.edu" type="cite">
<div style="margin:30px 25px 10px 25px;" class="__pbConvHr"><div
style="display:table;width:100%;border-top:1px solid
#EDEEF0;padding-top:5px"> <div
style="display:table-cell;vertical-align:middle;padding-right:6px;"><img
photoaddress="ems394@cornell.edu" photoname="Erich Marquard Schwarz"
src="cid:part1.04000008.06010902@googlemail.com"
name="compose-unknown-contact.jpg" height="25px" width="25px"></div> <div
style="display:table-cell;white-space:nowrap;vertical-align:middle;width:100%">
<a moz-do-not-send="true" href="mailto:ems394@cornell.edu"
style="color:#737F92
!important;padding-right:6px;font-weight:bold;text-decoration:none
!important;">Erich Marquard Schwarz</a></div> <div
style="display:table-cell;white-space:nowrap;vertical-align:middle;">
<font color="#9FA2A5"><span style="padding-left:6px">17 July 2014
20:12</span></font></div></div></div>
<div style="color:#888888;margin-left:24px;margin-right:24px;"
__pbrmquotes="true" class="__pbConvBody"><div><!----><br> For some
value of "supposed", but it is not optimal. If it could be corrected in
a future version of khmer, that would be good indeed!<br><br> I am
running a Perl script to retrofit the FastQ headers with '#0/1' and
'#0/2' (which was Illumina's older style of distinguishing paired-end
reads).<br><br><br>--Erich<br><br><br><br>_______________________________________________<br>khmer
mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br><a class="moz-txt-link-freetext" href="http://lists.idyll.org/listinfo/khmer">http://lists.idyll.org/listinfo/khmer</a><br></div></div>
<div style="margin:30px 25px 10px 25px;" class="__pbConvHr"><div
style="display:table;width:100%;border-top:1px solid
#EDEEF0;padding-top:5px"> <div
style="display:table-cell;vertical-align:middle;padding-right:6px;"><img
photoaddress="ems394@cornell.edu" photoname="Erich Marquard Schwarz"
src="cid:part1.04000008.06010902@googlemail.com"
name="compose-unknown-contact.jpg" height="25px" width="25px"></div> <div
style="display:table-cell;white-space:nowrap;vertical-align:middle;width:100%">
<a moz-do-not-send="true" href="mailto:ems394@cornell.edu"
style="color:#737F92
!important;padding-right:6px;font-weight:bold;text-decoration:none
!important;">Erich Marquard Schwarz</a></div> <div
style="display:table-cell;white-space:nowrap;vertical-align:middle;">
<font color="#9FA2A5"><span style="padding-left:6px">17 July 2014
18:19</span></font></div></div></div>
<div style="color:#888888;margin-left:24px;margin-right:24px;"
__pbrmquotes="true" class="__pbConvBody"><div>Hi all,<br><br>I used
khmer to begin normalizing RNA-seq data with this command:<br><br>
normalize-by-median.py -k 20 -C 20 -x 2e9 -N 4 --savehash
Csp1_rna_2014.07.16.filt.jumbled.kh Csp1_rna_2014.07.16.filt.jumbled.fa ;<br><br>which
produced Csp1_rna_2014.07.16.filt.jumbled.fa.keep.<br><br>Unfortunately,
I was not aware that khmer has the nasty side effect of stripping
header information. Here are two header texts -- the first from
Csp1_rna_2014.07.16.filt.jumbled.fa, the second from its khmer product
Csp1_rna_2014.07.16.filt.jumbled.fa.keep:<br><br>
>DHKW5DQ1:285:D1T8EACXX:7:1101:1397:2177 1:N:0:TATGTGGC<br><br>
>DHKW5DQ1:285:D1T8EACXX:7:1101:1397:2177<br><br>The first header line
has paired-end information using Illumina's new format (with trailing '
1' and ' 2' -- which I agree is less robust than the old-style '#1' and
'#2' suffixes that Illumina used to use, but Illumina is the 800-pound
gorilla here, and we are its mere servant chimps).<br><br>That
header-stripping 'feature' of khmer totally trashed my later work on the
data. I will have to retroname the reads (give them "#1' and "#2'
old-style suffixes) so that I can get khmer to work with them without
wrecking their usability for later re-sorting and subsequent uses (in
this case, genome RNA-scaffolding).<br><br>Lost time, roughly one day.<br><br>The
version I have of khmer was installed on 9/4/2012. If this side-effect
has been fixed since then, that's good news; if not, then it'd be good
if it *were* fixed.<br><br>Thank you,<br><br><br>--Erich<br><br><br><br>_______________________________________________<br>khmer
mailing list<br><a class="moz-txt-link-abbreviated" href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br><a class="moz-txt-link-freetext" href="http://lists.idyll.org/listinfo/khmer">http://lists.idyll.org/listinfo/khmer</a><br></div></div>
</blockquote>
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