[bi_maniac]

My histogram has 2 peaks in 149-150 and 200

#Mean 166,846
#Median 151
#Mode 200
#STDev 28,597
#PercentOfPairs 16,089
#InsertSize Count
51 1
57 1
69 3
73 1
75 1
76 1
79 1
82 2
86 1
87 1
88 1
91 1
92 1
95 1
96 1
97 1
98 4
101 1
103 3
105 1
106 4
107 2
109 2
111 3
112 4
113 2
114 3
115 9
116 6
117 3
118 13
119 3
120 4
121 17
122 3
123 8
124 18
125 12
126 15
127 16
128 10
129 13
130 16
131 8
132 12
133 17
134 19
135 16
136 26
137 25
138 18
139 48
140 31
141 32
142 39
143 35
144 49
145 53
146 98
147 160
148 217
149 398
150 379
151 240
152 175
153 114
154 57
155 32
156 17
157 8
158 5
159 2
160 2
161 1
162 1
163 1
164 1
165 2
166 1
167 3
168 4
169 1
170 2
172 5
175 1
176 1
177 3
178 4
179 2
180 5
181 5
182 4
183 12
184 4
185 7
186 3
187 7
188 13
189 14
190 15
191 18
192 31
193 37
194 52
195 79
196 82
197 92
198 267
199 170
200 405
201 154
202 52
203 31
204 22
205 6
206 3
207 3
208 1
209 1
210 2
211 3
214 1
216 1
217 3
218 1
221 4
231 1
238 1
240 1
241 2
249 1
256 1
257 1
260 2
263 3
264 2
265 2
266 2
273 1
282 3
284 2
286 2
287 2
288 2
289 2
290 1
291 3
292 1

[Brian Bushnell]

That would be very strange, for random shearing. Is it an amplicon library? If so, my previous post is irrelevant, it was based on the assumption of random shearing. Note that BBMerge can merge reads with insert size longer than read length using kmer counting, but that won't work for amplicons, only random fragmentation with sufficient coverage (>5x or so). Sometimes you can increase the merge rate by quality trimming (flags "qtrim2=r trimq=12" in BBMerge, which will only trim if the initial merge attempt fails), and for generating an insert size histogram of very low quality reads, I generally use the "xloose" flag which makes it more sensitive (at the expense of false positive merges).

What's the read quality like? Can you post the per-base qscore histogram? (reformat.sh in=reads.fq qhist=qhist.txt).

[bi_maniac]

Dear Brian.

I will continue giving you more info as soon as I get it.

Meanwhile let my give you many thanks for your most valuable help. Besides that I want to ask you for a further help:

Do you know any tutorial or book that I could read in order to learn thiese concepts. The bioinformatics books I have are too basic and do not treat these issues.

[Brian Bushnell]

Do you know any tutorial or book that I could read in order to learn these concepts. The bioinformatics books I have are too basic and do not treat these issues.

Sorry, I can't give you any advice there. Bioinformatics too rapidly-evolving now for books to be relevant for very long, I think.

[bi_maniac]

Hi Brian,

It is amplicon library. Insert range is 300-370. I will send you exec reports soon.

[bi_maniac]

Hi, helpful people: this conversation continues here: http://seqanswers.com/forums/showthread.php?t=63930

Thanks a lot.